From e127a9aac81a493eb413ee3cbd608acf133a6fa0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Thu, 7 Nov 2024 11:41:12 +0100 Subject: [PATCH 01/38] Add 1st draft for the microgalaxy lab --- communities/all/labs/microgalaxy | 1 + communities/microgalaxy/lab/CONTRIBUTORS | 3 + communities/microgalaxy/lab/README.md | 2 + communities/microgalaxy/lab/base.yml | 68 ++ .../microgalaxy/lab/sections/1_beginner.yml | 233 +++++ .../lab/sections/2_intermediate.yml | 36 + .../microgalaxy/lab/sections/3_advanced.yml | 80 ++ .../microgalaxy/lab/sections/4_community.yml | 31 + communities/microgalaxy/lab/static/custom.css | 0 .../lab/static/logo_single_cell.svg | 276 +++++ .../microgalaxy/lab/templates/conclusion.html | 45 + .../microgalaxy/lab/templates/footer.html | 0 .../microgalaxy/lab/templates/intro.html | 45 + .../microgalaxy/lab/tool_panel/hca-scanpy.yml | 16 + .../lab/tool_panel/hca-scanpy.yml.lock | 47 + .../lab/tool_panel/hicexplorer.yml | 120 +++ .../lab/tool_panel/hicexplorer.yml.lock | 359 +++++++ .../microgalaxy/lab/tool_panel/import.yml | 8 + .../lab/tool_panel/import.yml.lock | 23 + .../microgalaxy/lab/tool_panel/multiomics.yml | 4 + .../lab/tool_panel/multiomics.yml.lock | 11 + .../microgalaxy/lab/tool_panel/sccaf.yml | 10 + .../microgalaxy/lab/tool_panel/sccaf.yml.lock | 29 + .../microgalaxy/lab/tool_panel/seurat.yml | 28 + .../lab/tool_panel/seurat.yml.lock | 83 ++ .../lab/tool_panel/single_cell.yml | 136 +++ .../lab/tool_panel/single_cell.yml.lock | 568 +++++++++++ .../microgalaxy/lab/tool_panel/spatial.yml | 14 + .../lab/tool_panel/spatial.yml.lock | 41 + .../lab/tool_panel/tool_panel_view.yml | 438 ++++++++ .../lab/tool_panel/usegalaxy.org.au.yml | 964 ++++++++++++++++++ communities/microgalaxy/lab/usegalaxy.eu.yml | 55 + .../lab/usegalaxy.eu/static/custom.css | 10 + .../lab/usegalaxy.eu/templates/footer.html | 70 ++ .../microgalaxy/lab/usegalaxy.org.au.yml | 43 + .../usegalaxy.org.au/templates/footer.html | 119 +++ communities/microgalaxy/lab/usegalaxy.org.yml | 35 + 37 files changed, 4051 insertions(+) create mode 120000 communities/all/labs/microgalaxy create mode 100644 communities/microgalaxy/lab/CONTRIBUTORS create mode 100644 communities/microgalaxy/lab/README.md create mode 100644 communities/microgalaxy/lab/base.yml create mode 100644 communities/microgalaxy/lab/sections/1_beginner.yml create mode 100644 communities/microgalaxy/lab/sections/2_intermediate.yml create mode 100644 communities/microgalaxy/lab/sections/3_advanced.yml create mode 100644 communities/microgalaxy/lab/sections/4_community.yml create mode 100644 communities/microgalaxy/lab/static/custom.css create mode 100644 communities/microgalaxy/lab/static/logo_single_cell.svg create mode 100644 communities/microgalaxy/lab/templates/conclusion.html create mode 100644 communities/microgalaxy/lab/templates/footer.html create mode 100644 communities/microgalaxy/lab/templates/intro.html create mode 100644 communities/microgalaxy/lab/tool_panel/hca-scanpy.yml create mode 100644 communities/microgalaxy/lab/tool_panel/hca-scanpy.yml.lock create mode 100644 communities/microgalaxy/lab/tool_panel/hicexplorer.yml create mode 100644 communities/microgalaxy/lab/tool_panel/hicexplorer.yml.lock create mode 100644 communities/microgalaxy/lab/tool_panel/import.yml create mode 100644 communities/microgalaxy/lab/tool_panel/import.yml.lock create mode 100644 communities/microgalaxy/lab/tool_panel/multiomics.yml create mode 100644 communities/microgalaxy/lab/tool_panel/multiomics.yml.lock create mode 100644 communities/microgalaxy/lab/tool_panel/sccaf.yml create mode 100644 communities/microgalaxy/lab/tool_panel/sccaf.yml.lock create mode 100644 communities/microgalaxy/lab/tool_panel/seurat.yml create mode 100644 communities/microgalaxy/lab/tool_panel/seurat.yml.lock create mode 100644 communities/microgalaxy/lab/tool_panel/single_cell.yml create mode 100644 communities/microgalaxy/lab/tool_panel/single_cell.yml.lock create mode 100644 communities/microgalaxy/lab/tool_panel/spatial.yml create mode 100644 communities/microgalaxy/lab/tool_panel/spatial.yml.lock create mode 100644 communities/microgalaxy/lab/tool_panel/tool_panel_view.yml create mode 100644 communities/microgalaxy/lab/tool_panel/usegalaxy.org.au.yml create mode 100644 communities/microgalaxy/lab/usegalaxy.eu.yml create mode 100644 communities/microgalaxy/lab/usegalaxy.eu/static/custom.css create mode 100644 communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html create mode 100644 communities/microgalaxy/lab/usegalaxy.org.au.yml create mode 100644 communities/microgalaxy/lab/usegalaxy.org.au/templates/footer.html create mode 100644 communities/microgalaxy/lab/usegalaxy.org.yml diff --git a/communities/all/labs/microgalaxy b/communities/all/labs/microgalaxy new file mode 120000 index 00000000..db96afd0 --- /dev/null +++ b/communities/all/labs/microgalaxy @@ -0,0 +1 @@ +../../microgalaxy/lab \ No newline at end of file diff --git a/communities/microgalaxy/lab/CONTRIBUTORS b/communities/microgalaxy/lab/CONTRIBUTORS new file mode 100644 index 00000000..f1d71278 --- /dev/null +++ b/communities/microgalaxy/lab/CONTRIBUTORS @@ -0,0 +1,3 @@ +# If GitHub username, name and avatar will be fetched and displayed +bebatut +zierep \ No newline at end of file diff --git a/communities/microgalaxy/lab/README.md b/communities/microgalaxy/lab/README.md new file mode 100644 index 00000000..0105b125 --- /dev/null +++ b/communities/microgalaxy/lab/README.md @@ -0,0 +1,2 @@ +# microGalaxy subdomain/Lab + diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml new file mode 100644 index 00000000..d9fec4da --- /dev/null +++ b/communities/microgalaxy/lab/base.yml @@ -0,0 +1,68 @@ +# Request this as a webpage with: +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/base.yml + +# ----------------------------------------------------------------------------- +# Use these variables in HTML templates like: +# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}" +# To make the content more generic and reusable across sites + +# These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!" +site_name: Australia +lab_name: microGalaxy Lab +analysis_name: microGalaxy +nationality: Australian + +# Used for rendering tool/workflow links. Trailing '/' will be removed. +galaxy_base_url: https://singlecell.usegalaxy.org +subdomain: singlecell +root_domain: usegalaxy.org + +# This will enable a feedback form on the webpage: +# feedback_email: help@mygalaxy.org + +support_url: https://help.galaxyproject.org +# quota_request_url: https://help.galaxyproject.org +data_policy_url: https://usegalaxy.org/static/terms.html +terms_url: https://usegalaxy.org/static/terms.html + +help_links: + - title: General Galaxy support + url: https://galaxyproject.org/support/ + - title: Single Cell help forum + url: https://help.galaxyproject.org/tag/single-cell + - title: General Galaxy help forum + url: https://help.galaxyproject.org + - title: Galaxy Training Network Slack workspace + url: https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg + - title: Single cell Slack channel (#single-cell-users) + url: https://gtnsmrgsbord.slack.com/archives/C06PBRR40D7 + - title: Single cell user community chat room (Same channel but using Matrix/Element) + url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - title: Galaxy Training Community chat + url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im + - title: Usegalaxy.org chat + url: https://matrix.to/#/#galaxyproject_Lobby:gitter.im + +intro_extra_md: "" +conclusion_extra_md: "" + +# ----------------------------------------------------------------------------- +# Custom content relative to this file URL + +header_logo: static/logo_single_cell.svg +custom_css: static/custom.css +intro_md: templates/intro.html +conclusion_md: templates/conclusion.html +footer_md: templates/footer.html + + +# Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements. +# Either: +# 1. Relative to this file URL +# 2. Full URL to fetch globally centralized content +sections: + - sections/1_beginner.yml + - sections/3_advanced.yml + - sections/4_community.yml + +# ----------------------------------------------------------------------------- diff --git a/communities/microgalaxy/lab/sections/1_beginner.yml b/communities/microgalaxy/lab/sections/1_beginner.yml new file mode 100644 index 00000000..d4aac6a8 --- /dev/null +++ b/communities/microgalaxy/lab/sections/1_beginner.yml @@ -0,0 +1,233 @@ +id: beginner +title: Learn to use Galaxy for microbial data analysis +tabs: + - id: learning_pathway + title: Learning pathways + heading_md: > + Connected tutorials to train you to perform single-cell analysis fast! + content: + - title_md: Introduction to Galaxy and Sequence analysis + description_md: > + This learning path aims to teach you the basics of Galaxy and analysis of sequencing data. You will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences. + + New to Galaxy and/or the field of genomics? Follow this {gtn modal}[learning path to get familiar with the basics](https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html)! + button_link: https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html + button_icon: tutorial + button_tip: Go to learning pathway + - title_md: Genome annotation for prokaryotes + description_md: > + Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo. + Check out the {gtn modal}[Genome annotation for prokaryotes learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html). + button_link: https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html + button_icon: tutorial + button_tip: Go to learning pathway + - title_md: Detection of AMR genes in bacterial genomes + description_md: > + This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy. + + Check out the {gtn modal}[Detection of AMR genes in bacterial genomes learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html). + button_link: https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html + button_icon: tutorial + button_tip: Go to learning pathway + - title_md: Metagenomics data processing and analysis for microbiome + description_md: > + This learning path aims to teach you the basics of Galaxy and analysis of metagenomics data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of microbiome data analysis: quality control, taxonomic profiling, taxonomic binning, assembly, functional profiling, and also some applications + + Check out the {gtn modal}[Metagenomics data processing and analysis for microbiome learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html). + button_link: https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html + button_tip: Go to learning pathway + button_icon: tutorial + - title_md: Clinical metaproteomics workflows within Galaxy + description_md: > + This learning path aims to teach you the basics of how to perform metaproteomics analysis of the clinical data within the Galaxy platform. You will learn how to use Galaxy for analysis and will be guided through the most common first steps of any metaproteomics database generation to searching the database, verifying the proteins/peptides, and data analysis. + + Check out the {gtn modal}[Clinical metaproteomics workflows within Galaxy learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html). + button_link: https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html + button_tip: View training menu + button_icon: tutorial + + - id: bacterial_genomics_tutorial + title: Bacterial genomics tutorials + heading_md: > + Using public data is free! Learn how to retrieve data from common sources. + content: + - title_md: Importing files from the Single Cell Expression Atlas + description_md: > + You can import data directly from the Single Cell Expression Atlas with one tool. You will need an **experiment accession** ID, which you can find by browsing experiments at the [EBI Atlas site](https://www.ebi.ac.uk/gxa/sc/experiments). Input that **experiment accession** ID in the *Tool Parameters* box when of the following tool. Then **Run tool** to get your matrix! + EBI SCXA Data Retrieval + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fretrieve_scxa%2fretrieve_scxa" + button_icon: run + button_tip: Run tool + - title_md: Importing from public atlases - Tutorial + description_md: > + You can learn more by following our dedicated to tutorial for importing files from public atlases. + button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/tutorial.html + button_icon: tutorial + button_tip: View tutorial + - title_md: Importing from NCBI/GEO + description_md: > + Where there isn't a specific tool for retrieving data, you can nevertheless import and reformat data from the commonly used NCBI/GEO repository with the following tutorial. + button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html + button_icon: tutorial + button_tip: View tutorial + - title_md: Importing 10X Files + description_md: > + You can find many tools for importing 10X formatted data into target datatypes. + Scanpy Read10x + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_read_10x%2fscanpy_read_10x" + button_icon: run + button_tip: Run tool + - title_md: Seurat Read10x + description_md: > + Import 10X formatted data into a Seurat object. Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_read10x%2fseurat_read10x" + button_icon: run + button_tip: Run tool + - title_md: DropletUtils Read10x + description_md: > + DropletUtils 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. + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fdropletutils_read_10x%2fdropletutils_read_10x" + button_icon: run + button_tip: Run tool + + - id: data_convert + title: Converting datatypes + heading_md: > + Single-cell data comes in many formats. + Here we show a few key tools in Galaxy for converting and manipulating objects in Galaxy. + content: + - title_md: SCEasy Converter + description_md: > + This tool allows you to convert between the following formats: + + - `hdf5` (AnnData/Loom) + - `rds` (Seurat) + - `rdata.sce` (Single Cell Experiment) + - `h5` (Seurat) + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/sceasy_convert%2fsceasy_convert" + button_icon: run + button_tip: Run tool + - title_md: Manipulate AnnData + description_md: > + Under the parameter `Function to manipulate the object` you'll find key manipulations for AnnData, such as: + + - `Concatenate along the observations axis` for combining AnnData objects together + - `Transpose the data matrix` for help with converting formats + - `Filter observations or variables` for refining or subsetting your dataset + - `Adding annotations` and `Rename categories` for manipulating metadata + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/anndata_manipulate%2fanndata_manipulate" + button_icon: run + button_tip: Run tool + - title_md: AnnData Operations + description_md: > + This tool allows you to flag genes (such as mitochondrial genes) as well as change names in the metadata. + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fanndata_ops%2fanndata_ops" + button_icon: run + button_tip: Run tool + - title_md: Data conversion training + description_md: > + You can also explore our dedicated tutorial on single-cell data conversion. + button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" + button_icon: tutorial + button_tip: View tutorial + + - id: data_viz + title: Visualising Data + heading_md: > + There are a few key tools for visualising single-cell data in Galaxy. + content: + - title_md: Plot with Scanpy + description_md: > + This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots. + inputs: + - label: Single cell data + datatypes: + - hdf5 (AnnData) + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/scanpy_plot%2fscanpy_plot" + button_icon: run + button_tip: Run tool + - title_md: Scanpy PlotEmbed + description_md: > + This tool allows you to plot embeddings like UMAPs. + inputs: + - label: Single cell data + datatypes: + - hdf5 (AnnData) + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_plot_embed%2fscanpy_plot_embed" + button_icon: run + button_tip: Run tool + - title_md: Scanpy PlotTrajectory + description_md: > + This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object. + inputs: + - label: Single cell data + datatypes: + - hdf5 (AnnData) + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxi%2fscanpy_plot_trajectory/scanpy_plot_trajectory" + button_icon: run + button_tip: Run tool + - title_md: Scanpy Plot dimension reduction + description_md: > + This tool allows you to plot embeddings such as PCA, UMAP, and tSNE. + inputs: + - label: Single cell data + datatypes: + - rds (Seurat object) + - rdata.sce (Single Cell Experiment) + - h5 (Seurat) + - hdf5 (Loom/AnnData) + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_dim_plot%2fseurat_dim_plot" + button_icon: run + button_tip: Run tool + - title_md: Plot with Seurat + description_md: > + This tool allows you to plot gene expressions, such as with Violin Plots. + inputs: + - label: Single cell data + datatypes: + - rds (Seurat object) + - rdata.sce (Single Cell Experiment) + - h5 (Seurat) + - hdf5 (Loom/AnnData) + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_plot%2fseurat_plot" + button_icon: run + button_tip: Run tool + + - id: help + title: Help + content: + - title_md: Single Cell help forum + description_md: > + Of course! Check out the Galaxy Project + [Single cell help forum](https://help.galaxyproject.org/tag/scrna) + - title_md: Troubleshooting errors + description_md: > + Find specific advice for + {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) + on the GTN. + - title_md: Can I upload sensitive data? + description_md: > + No, please do not upload personal or sensitive, such as human health or clinical data. Please see our + [Privacy Policy]({{ data_policy_url }}) + page for definitions of sensitive and health-related information. + + Please also make sure you have read our + [Terms of Service]({{ terms_url }}), + which covers hosting and analysis of research data. + - title_md: Is my data private? + description_md: > + Please read our + [Privacy Policy]({{ data_policy_url }}) + for information on your personal data and any data that you upload. + - title_md: How can I increase my storage quota? + description_md: > + Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request. + button_md: Request + button_link: "{{ quota_request_url }}" + exclude_from: + - usegalaxy.org + - title_md: Galaxy {{ site_name }} support + description_md: > + Any user of Galaxy {{ site_name }} can request support online! + button_md: Request support + button_link: "{{ support_url }}" diff --git a/communities/microgalaxy/lab/sections/2_intermediate.yml b/communities/microgalaxy/lab/sections/2_intermediate.yml new file mode 100644 index 00000000..f9cc27ae --- /dev/null +++ b/communities/microgalaxy/lab/sections/2_intermediate.yml @@ -0,0 +1,36 @@ +id: intermediate +title: Advanced analysis +tabs: + - id: workflows + title: Multiomic Analyses + content: + - title_md: These tutorials use different methods to analyse scRNA-seq samples. + description_md: > + {gtn modal}[Learn more](https://training.galaxyproject.org/training-material/topics/single-cell/#st-end-to-end/) + + + + - id: deconvolution + title: Deconvolution + heading_md: > + These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference + These tutorials use different methods to analyse scRNA-seq samples. + Learn more. + content: [] + + - id: tips + title: Tips, tricks & other hints + heading_md: > + These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference + These tutorials use different methods to analyse scRNA-seq samples. + Learn more. + content: + - title_md: About these workflows + description_md: > + Hello! Mehmet working here + button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html#tip-creating-a-new-history + button_tip: View tutorial + button_icon: tutorial + - title_md: Spare space for another GTN + description_md: > + More GTN diff --git a/communities/microgalaxy/lab/sections/3_advanced.yml b/communities/microgalaxy/lab/sections/3_advanced.yml new file mode 100644 index 00000000..bf837dac --- /dev/null +++ b/communities/microgalaxy/lab/sections/3_advanced.yml @@ -0,0 +1,80 @@ +id: advanced +title: Workflows +tabs: + - id: workflows1 + title: Workflow Best Practices + heading_md: > +
+

+ Workflows are chains of of tools that can be run together at the click of a button. + The above tabs contain both peer reviewed and community submitted workflows. +

+

+ Tag your workflows + with #microgalaxy and share publicly with other users! +

+ Additional common workflow tags for our community are: + +
+ + content: + - title_md: How to tag a workflow + description_md: > + + - title_md: WorkflowHub + description_md: > + WorkflowHub hosts high quality workflows. You can explore microGalaxy workflows from WorkflowHub. + button_link: "https://workflowhub.eu/search?q=microgalaxy+galaxy" + button_md: đź”— + button_tip: Visit WorkflowHub + - id: workflows3 + title: Community workflows + heading_md: > + Anyone on Galaxy can share their workflow publicly - if your workflow is running well, share it with others! +

You can search these community workflows below.

+ content: + - title_md: Community Workflows + description_md: > + Search through community workflows tagged with #microgalaxy. + + + - title_md: Advanced workflow search + description_md: > + The GTN's + {gtn modal}[Pan-Galactic Workflow Search](https://training.galaxyproject.org/training-material/workflows/list.html) + allows you to search for workflows across all of Galaxy! + + button_link: "https://training.galaxyproject.org/training-material/workflows/list.html" + button_md: 🔗 + button_tip: Visit WorkflowHub + + - title_md: How to share your workflow + description_md: > + Learn how to {gtn modal}[publish your workflow](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_publish.html) + to share your work with the Galaxy community. diff --git a/communities/microgalaxy/lab/sections/4_community.yml b/communities/microgalaxy/lab/sections/4_community.yml new file mode 100644 index 00000000..16349ee3 --- /dev/null +++ b/communities/microgalaxy/lab/sections/4_community.yml @@ -0,0 +1,31 @@ +id: community +title: Community +tabs: + - id: participate + title: Participate + content: + - title_md: Chat with other users + description_md: > + Check out some suggestions on how you can + {gtn modal}[connect with the community](https://training.galaxyproject.org/training-material/topics/single-cell/faqs/user_community_join.html). + - title_md: Join our community! + description_md: > + + This Galaxy space is the result of hard, collaborative work by many contributors . + + It is maintained by the [Galaxy Single-cell & sPatial Omics **SPOC** Community of Practice](https://galaxyproject.org/community/sig/singlecell/). + + This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make single-cell & spatial omics analysis easier. + + Check out our site and join our community! + + button_link: "https://galaxyproject.org/community/sig/singlecell/" + button_md: 🖖🏽 + button_tip: Visit SPOC + - id: governance + title: How is the Galaxy Community organised? + content: + heading_md: > + Learn about the + {gtn modal}[governance structure of Galaxy communities](https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html) on the GTN. + content: [] diff --git a/communities/microgalaxy/lab/static/custom.css b/communities/microgalaxy/lab/static/custom.css new file mode 100644 index 00000000..e69de29b diff --git a/communities/microgalaxy/lab/static/logo_single_cell.svg b/communities/microgalaxy/lab/static/logo_single_cell.svg new file mode 100644 index 00000000..43540c2b --- /dev/null +++ b/communities/microgalaxy/lab/static/logo_single_cell.svg @@ -0,0 +1,276 @@ + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/communities/microgalaxy/lab/templates/conclusion.html b/communities/microgalaxy/lab/templates/conclusion.html new file mode 100644 index 00000000..b751908f --- /dev/null +++ b/communities/microgalaxy/lab/templates/conclusion.html @@ -0,0 +1,45 @@ +{% load markdown %} + +
+ {% if help_links %} +

Single Cell and Spatial Omics community support

+ + {% endif %} +
+ +
+

News and Events

+ +
+
+ +
+
+ +
+
+
+ +{% if feedback_email %} +
+

What do you think of the {{ lab_name }}?

+ +
+{% endif %} + + +
+ {{ conclusion_extra_md|safe }} +
diff --git a/communities/microgalaxy/lab/templates/footer.html b/communities/microgalaxy/lab/templates/footer.html new file mode 100644 index 00000000..e69de29b diff --git a/communities/microgalaxy/lab/templates/intro.html b/communities/microgalaxy/lab/templates/intro.html new file mode 100644 index 00000000..625c1d4d --- /dev/null +++ b/communities/microgalaxy/lab/templates/intro.html @@ -0,0 +1,45 @@ +
+

+ Welcome to the Galaxy {{ site_name }} {{ lab_name }}! +

+ +

+ Whether you are analysing microbiome samples or bacterial isolates, long reads or short, shotgun or 16S, genomics, transcriptomics, proteomics or metabolomics, multiomics or integrative analysis this is the place to be! +

+

+ + How does this page relate to Galaxy {{ site_name }}? + +

+ + {{ intro_extra_md }} + + +
diff --git a/communities/microgalaxy/lab/tool_panel/hca-scanpy.yml b/communities/microgalaxy/lab/tool_panel/hca-scanpy.yml new file mode 100644 index 00000000..30e12240 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/hca-scanpy.yml @@ -0,0 +1,16 @@ +tool_panel_section_label: HCA-Scanpy +tools: +- name: seurat_plot + owner: ebi-gxa +- name: scanpy_integrate_bbknn + owner: ebi-gxa +- name: scanpy_integrate_combat + owner: ebi-gxa +- name: scanpy_integrate_mnn + owner: ebi-gxa +- name: scanpy_plot_scrublet + owner: ebi-gxa +- name: scanpy_multiplet_scrublet + owner: ebi-gxa +- name: seurat_run_umap + owner: ebi-gxa diff --git a/communities/microgalaxy/lab/tool_panel/hca-scanpy.yml.lock b/communities/microgalaxy/lab/tool_panel/hca-scanpy.yml.lock new file mode 100644 index 00000000..62bc2659 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/hca-scanpy.yml.lock @@ -0,0 +1,47 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: HCA-Scanpy +tools: +- name: seurat_plot + owner: ebi-gxa + revisions: + - 95d79f1134f0 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_integrate_bbknn + owner: ebi-gxa + revisions: + - c9da9192eee5 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_integrate_combat + owner: ebi-gxa + revisions: + - 3c47bc560688 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_integrate_mnn + owner: ebi-gxa + revisions: + - ff6decc0f432 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_plot_scrublet + owner: ebi-gxa + revisions: + - 6f5509cf3176 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_multiplet_scrublet + owner: ebi-gxa + revisions: + - 53ce0e336840 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: seurat_run_umap + owner: ebi-gxa + revisions: + - b9424c715a0d + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy diff --git a/communities/microgalaxy/lab/tool_panel/hicexplorer.yml b/communities/microgalaxy/lab/tool_panel/hicexplorer.yml new file mode 100644 index 00000000..7c94a0de --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/hicexplorer.yml @@ -0,0 +1,120 @@ +tool_panel_section_label: HiCExplorer +tools: +- name: hicexplorer_chicaggregatestatistic + owner: bgruening +- name: hicexplorer_chicdifferentialtest + owner: bgruening +- name: hicexplorer_chicexportdata + owner: bgruening +- name: hicexplorer_chicplotviewpoint + owner: bgruening +- name: hicexplorer_chicqualitycontrol + owner: bgruening +- name: hicexplorer_chicsignificantinteractions + owner: bgruening +- name: hicexplorer_chicviewpoint + owner: bgruening +- name: hicexplorer_chicqualitycontrol + owner: bgruening +- name: hicexplorer_chicsignificantinteractions + owner: bgruening +- name: hicexplorer_chicviewpoint + owner: bgruening +- name: hicexplorer_chicviewpointbackgroundmodel + owner: bgruening +- name: hicexplorer_hicadjustmatrix + owner: bgruening +- name: hicexplorer_hicaggregatecontacts + owner: bgruening +- name: hicexplorer_hicaverageregions + owner: bgruening +- name: hicexplorer_hicbuildmatrix + owner: bgruening +- name: hicexplorer_hiccomparematrices + owner: bgruening +- name: hicexplorer_hiccompartmentspolarization + owner: bgruening +- name: hicexplorer_hicconvertformat + owner: bgruening +- name: hicexplorer_hiccorrectmatrix + owner: bgruening +- name: hicexplorer_hiccorrelate + owner: bgruening +- name: hicexplorer_hicdetectloops + owner: bgruening +- name: hicexplorer_hicdifferentialtad + owner: bgruening +- name: hicexplorer_hicfindrestrictionsites + owner: bgruening +- name: hicexplorer_hicfindtads + owner: bgruening +- name: hicexplorer_hichyperoptdetectloops + owner: bgruening +- name: hicexplorer_hicinfo + owner: bgruening +- name: hicexplorer_hicinterintratad + owner: bgruening +- name: hicexplorer_hicmergedomains + owner: bgruening +- name: hicexplorer_hicmergeloops + owner: bgruening +- name: hicexplorer_hicmergematrixbins + owner: bgruening +- name: hicexplorer_hicnormalize + owner: bgruening +- name: hicexplorer_hicpca + owner: bgruening +- name: hicexplorer_hicplotaverageregions + owner: bgruening +- name: hicexplorer_hicplotdistvscounts + owner: bgruening +- name: hicexplorer_hicplotmatrix + owner: bgruening +- name: hicexplorer_hicplotsvl + owner: bgruening +- name: hicexplorer_hicplotviewpoint + owner: bgruening +- name: hicexplorer_hicquickqc + owner: bgruening +- name: hicexplorer_hicsummatrices + owner: bgruening +- name: hicexplorer_hictadclassifier + owner: bgruening +- name: hicexplorer_hictraintadclassifier + owner: bgruening +- name: hicexplorer_hictransform + owner: bgruening +- name: hicexplorer_hicvalidatelocations + owner: bgruening +- name: schicexplorer_schicadjustmatrix + owner: iuc +- name: schicexplorer_schiccluster + owner: iuc +- name: schicexplorer_schicclustercompartments + owner: iuc +- name: schicexplorer_schicclusterminhash + owner: iuc +- name: schicexplorer_schicclustersvl + owner: iuc +- name: schicexplorer_schicconsensusmatrices + owner: iuc +- name: schicexplorer_schiccorrectmatrices + owner: iuc +- name: schicexplorer_schiccreatebulkmatrix + owner: iuc +- name: schicexplorer_schicdemultiplex + owner: iuc +- name: schicexplorer_schicinfo + owner: iuc +- name: schicexplorer_schicmergematrixbins + owner: iuc +- name: schicexplorer_schicmergetoscool + owner: iuc +- name: schicexplorer_schicnormalize + owner: iuc +- name: schicexplorer_schicplotclusterprofiles + owner: iuc +- name: schicexplorer_schicplotconsensusmatrices + owner: iuc +- name: schicexplorer_schicqualitycontrol + owner: iuc diff --git a/communities/microgalaxy/lab/tool_panel/hicexplorer.yml.lock b/communities/microgalaxy/lab/tool_panel/hicexplorer.yml.lock new file mode 100644 index 00000000..a86a55c1 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/hicexplorer.yml.lock @@ -0,0 +1,359 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: HiCExplorer +tools: +- name: hicexplorer_chicaggregatestatistic + owner: bgruening + revisions: + - 01c37e54e86e + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicdifferentialtest + owner: bgruening + revisions: + - 9d42a6133690 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicexportdata + owner: bgruening + revisions: + - 23b8d6b8960c + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicplotviewpoint + owner: bgruening + revisions: + - 013e53ccc7ac + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicqualitycontrol + owner: bgruening + revisions: + - b892fa1fcaec + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicsignificantinteractions + owner: bgruening + revisions: + - 640e0e45518a + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicviewpoint + owner: bgruening + revisions: + - f881c94fb3b3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicqualitycontrol + owner: bgruening + revisions: + - b892fa1fcaec + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicsignificantinteractions + owner: bgruening + revisions: + - 640e0e45518a + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicviewpoint + owner: bgruening + revisions: + - f881c94fb3b3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicviewpointbackgroundmodel + owner: bgruening + revisions: + - 9d02f1819e81 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicadjustmatrix + owner: bgruening + revisions: + - 2dccb6bb0add + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicaggregatecontacts + owner: bgruening + revisions: + - f0216498a666 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicaverageregions + owner: bgruening + revisions: + - c72fa6cb8817 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicbuildmatrix + owner: bgruening + revisions: + - ed2cca6b5de4 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hiccomparematrices + owner: bgruening + revisions: + - 3ee5332bf57c + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hiccompartmentspolarization + owner: bgruening + revisions: + - 3a6a5381db36 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicconvertformat + owner: bgruening + revisions: + - c0737631eea1 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hiccorrectmatrix + owner: bgruening + revisions: + - ea19190ce5e0 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hiccorrelate + owner: bgruening + revisions: + - 2b4d6a8dab36 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicdetectloops + owner: bgruening + revisions: + - 0410b6aada45 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicdifferentialtad + owner: bgruening + revisions: + - 77d8e0fd162a + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicfindrestrictionsites + owner: 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tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicclustersvl + owner: iuc + revisions: + - e6ec3914a076 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicconsensusmatrices + owner: iuc + revisions: + - 33b1c99cc709 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schiccorrectmatrices + owner: iuc + revisions: + - 295558e266d0 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schiccreatebulkmatrix + owner: iuc + revisions: + - acb3ed49109e + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicdemultiplex + owner: iuc + revisions: + - f224fc9af1d3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicinfo + owner: iuc + revisions: + - 41b415c410e3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicmergematrixbins + owner: iuc + revisions: + - 47ef02546fe9 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicmergetoscool + owner: iuc + revisions: + - 70a13d0a950f + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicnormalize + owner: iuc + revisions: + - 66e96c3d3c5d + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicplotclusterprofiles + owner: iuc + revisions: + - 65f2f5d29947 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicplotconsensusmatrices + owner: iuc + revisions: + - 95b1216e1e70 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicqualitycontrol + owner: iuc + revisions: + - 4a841ab67e3b + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer diff --git a/communities/microgalaxy/lab/tool_panel/import.yml b/communities/microgalaxy/lab/tool_panel/import.yml new file mode 100644 index 00000000..f87138d9 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/import.yml @@ -0,0 +1,8 @@ +tool_panel_section_label: Import/manipulate sc data +tools: +- name: 10x_bamtofastq + owner: bgruening +- name: scater_read_10x_results + owner: ebi-gxa +- name: gsc_scran_normalize + owner: artbio diff --git a/communities/microgalaxy/lab/tool_panel/import.yml.lock b/communities/microgalaxy/lab/tool_panel/import.yml.lock new file mode 100644 index 00000000..8b5f8cd3 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/import.yml.lock @@ -0,0 +1,23 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Import/manipulate sc data +tools: +- name: 10x_bamtofastq + owner: bgruening + revisions: + - f71fd828c126 + tool_panel_section_id: import_manipulate_sc_data + tool_panel_section_label: Import/manipulate sc data +- name: scater_read_10x_results + owner: ebi-gxa + revisions: + - da3f394039b5 + tool_panel_section_id: import_manipulate_sc_data + tool_panel_section_label: Import/manipulate sc data +- name: gsc_scran_normalize + owner: artbio + revisions: + - 6864acb21714 + tool_panel_section_id: import_manipulate_sc_data + tool_panel_section_label: Import/manipulate sc data diff --git a/communities/microgalaxy/lab/tool_panel/multiomics.yml b/communities/microgalaxy/lab/tool_panel/multiomics.yml new file mode 100644 index 00000000..e305aae5 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/multiomics.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Multiomics +tools: +- name: episcanpy_cluster_embed + owner: iuc diff --git a/communities/microgalaxy/lab/tool_panel/multiomics.yml.lock b/communities/microgalaxy/lab/tool_panel/multiomics.yml.lock new file mode 100644 index 00000000..467ea6c6 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/multiomics.yml.lock @@ -0,0 +1,11 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Multiomics +tools: +- name: episcanpy_cluster_embed + owner: iuc + revisions: + - f4713992f23a + tool_panel_section_id: multiomics + tool_panel_section_label: Multiomics diff --git a/communities/microgalaxy/lab/tool_panel/sccaf.yml b/communities/microgalaxy/lab/tool_panel/sccaf.yml new file mode 100644 index 00000000..45909169 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/sccaf.yml @@ -0,0 +1,10 @@ +tool_panel_section_label: SCCAF +tools: +- name: run_sccaf + owner: ebi-gxa +- name: sccaf_asses + owner: ebi-gxa +- name: sccaf_asses_merger + owner: ebi-gxa +- name: sccaf_regress_out + owner: ebi-gxa diff --git a/communities/microgalaxy/lab/tool_panel/sccaf.yml.lock b/communities/microgalaxy/lab/tool_panel/sccaf.yml.lock new file mode 100644 index 00000000..49c80525 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/sccaf.yml.lock @@ -0,0 +1,29 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: SCCAF +tools: +- name: run_sccaf + owner: ebi-gxa + revisions: + - 647d34f125bc + tool_panel_section_id: sccaf + tool_panel_section_label: SCCAF +- name: sccaf_asses + owner: ebi-gxa + revisions: + - 37a4c22f600b + tool_panel_section_id: sccaf + tool_panel_section_label: SCCAF +- name: sccaf_asses_merger + owner: ebi-gxa + revisions: + - 99d15ded4d5f + tool_panel_section_id: sccaf + tool_panel_section_label: SCCAF +- name: sccaf_regress_out + owner: ebi-gxa + revisions: + - 5ef0610e9f50 + tool_panel_section_id: sccaf + tool_panel_section_label: SCCAF diff --git a/communities/microgalaxy/lab/tool_panel/seurat.yml b/communities/microgalaxy/lab/tool_panel/seurat.yml new file mode 100644 index 00000000..0b95e939 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/seurat.yml @@ -0,0 +1,28 @@ +tool_panel_section_label: Seurat +tools: +- name: seurat_create_seurat_object + owner: ebi-gxa +- name: seurat_export_cellbrowser + owner: ebi-gxa +- name: seurat_filter_cells + owner: ebi-gxa +- name: seurat_find_clusters + owner: ebi-gxa +- name: seurat_find_markers + owner: ebi-gxa +- name: seurat_find_neighbours + owner: ebi-gxa +- name: seurat_find_variable_genes + owner: ebi-gxa +- name: seurat_normalise_data + owner: ebi-gxa +- name: seurat_dim_plot + owner: ebi-gxa +- name: seurat_read10x + owner: ebi-gxa +- name: seurat_run_pca + owner: ebi-gxa +- name: seurat_run_tsne + owner: ebi-gxa +- name: seurat_scale_data + owner: ebi-gxa diff --git a/communities/microgalaxy/lab/tool_panel/seurat.yml.lock b/communities/microgalaxy/lab/tool_panel/seurat.yml.lock new file mode 100644 index 00000000..cf910f55 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/seurat.yml.lock @@ -0,0 +1,83 @@ 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tool_panel_section_label: Seurat +- name: seurat_find_variable_genes + owner: ebi-gxa + revisions: + - 948fc0276b4f + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_normalise_data + owner: ebi-gxa + revisions: + - 3f49bc9c9213 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_dim_plot + owner: ebi-gxa + revisions: + - 64174ac50d78 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_read10x + owner: ebi-gxa + revisions: + - f5db0e853f57 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_run_pca + owner: ebi-gxa + revisions: + - 8ded486b0014 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_run_tsne + owner: ebi-gxa + revisions: + - 0db997e4a81d + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_scale_data + owner: ebi-gxa + revisions: + - 5e9ba303f9e1 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat diff --git a/communities/microgalaxy/lab/tool_panel/single_cell.yml b/communities/microgalaxy/lab/tool_panel/single_cell.yml new file mode 100644 index 00000000..a8a11fed --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/single_cell.yml @@ -0,0 +1,136 @@ +tool_panel_section_label: Single-cell +tools: +- name: scanpy_plot + owner: iuc +- name: scanpy_inspect + owner: iuc +- name: scanpy_filter + owner: iuc +- name: scanpy_normalize + owner: iuc +- name: scanpy_cluster_reduce_dimension + owner: iuc +- name: scanpy_remove_confounders + owner: iuc +- name: anndata_export + owner: iuc +- name: anndata_import + owner: iuc +- name: anndata_inspect + owner: iuc +- name: anndata_manipulate + owner: iuc +- name: modify_loom + owner: iuc +- name: dropletutils + owner: iuc +- name: raceid_clustering + owner: iuc +- name: raceid_filtnormconf + owner: iuc +- name: raceid_inspectclusters + owner: iuc +- name: raceid_inspecttrajectory + owner: iuc +- name: raceid_trajectory + owner: iuc +- name: scanpy_filter_cells + owner: ebi-gxa +- name: scanpy_filter_genes + owner: ebi-gxa +- name: scanpy_normalise_data + owner: ebi-gxa +- name: scanpy_find_variable_genes + owner: ebi-gxa +- name: scanpy_scale_data + owner: ebi-gxa +- name: scanpy_run_pca + owner: ebi-gxa +- name: scanpy_compute_graph + owner: ebi-gxa +- name: scanpy_run_tsne + owner: ebi-gxa +- name: scanpy_run_umap + owner: ebi-gxa +- name: scanpy_find_cluster + owner: ebi-gxa +- name: scanpy_find_markers + owner: ebi-gxa +- name: scanpy_plot_embed + owner: ebi-gxa +- name: anndata_ops + owner: ebi-gxa +- name: scanpy_parameter_iterator + owner: ebi-gxa +- name: scanpy_read_10x + owner: ebi-gxa +- name: scanpy_integrate_harmony + owner: ebi-gxa +- name: gtf2gene_list + owner: ebi-gxa +- name: scanpy_run_fdg + owner: ebi-gxa +- name: scanpy_run_diffmap + owner: ebi-gxa +- name: scanpy_run_paga + owner: ebi-gxa +- name: scanpy_run_dpt + owner: ebi-gxa +- name: scanpy_plot_trajectory 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tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: snapatac2_peaks_and_motif + owner: iuc + revisions: + - 588c811fdd48 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: snapatac2_plotting + owner: iuc + revisions: + - fecf9664c885 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: snapatac2_preprocessing + owner: iuc + revisions: + - cec3e76eaf05 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell diff --git a/communities/microgalaxy/lab/tool_panel/spatial.yml b/communities/microgalaxy/lab/tool_panel/spatial.yml new file mode 100644 index 00000000..85d64f88 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/spatial.yml @@ -0,0 +1,14 @@ +tool_panel_section_label: Spatial +tools: +- name: quantification + owner: perssond +- name: cell_intensity_processing + owner: goeckslab +- name: s3segmenter + owner: perssond +- name: slice_image + owner: imgteam +- name: squidpy + owner: goeckslab +- name: vitessce_spatial + owner: goeckslab diff --git a/communities/microgalaxy/lab/tool_panel/spatial.yml.lock b/communities/microgalaxy/lab/tool_panel/spatial.yml.lock new file mode 100644 index 00000000..415c67d3 --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/spatial.yml.lock @@ -0,0 +1,41 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Spatial +tools: +- name: quantification + owner: perssond + revisions: + - 3a916c4e9f5f + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: cell_intensity_processing + owner: goeckslab + revisions: + - 5d541df02496 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: s3segmenter + owner: perssond + revisions: + - 96d0d969ebc9 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: slice_image + owner: imgteam + revisions: + - a72590196440 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: squidpy + owner: goeckslab + revisions: + - d30ef0613122 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: vitessce_spatial + owner: goeckslab + revisions: + - 7cc457aa78b1 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial diff --git a/communities/microgalaxy/lab/tool_panel/tool_panel_view.yml b/communities/microgalaxy/lab/tool_panel/tool_panel_view.yml new file mode 100644 index 00000000..992f462b --- /dev/null +++ b/communities/microgalaxy/lab/tool_panel/tool_panel_view.yml @@ -0,0 +1,438 @@ +name: Single Cell +type: generic +id: singlecell +items: +- id: general_section + text: General Tools + type: label +- sections: + # These will be named differently on each server: + - getext # "Get Data" + - send # "Send Data" + - collection_operations + - plots + - textutil + - filter + - group +- id: sc_tools + text: Single Cell Tools + type: label +- id: importSC + name: 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+ tool_panel_section_label: Single-Cell +- name: hicexplorer_hicaverageregions + owner: bgruening + revisions: + - c72fa6cb8817 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicbuildmatrix + owner: bgruening + revisions: + - ed2cca6b5de4 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hiccomparematrices + owner: bgruening + revisions: + - 3ee5332bf57c + tool_panel_section_label: Single-Cell +- name: hicexplorer_hiccompartmentspolarization + owner: bgruening + revisions: + - 3a6a5381db36 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicconvertformat + owner: bgruening + revisions: + - c0737631eea1 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hiccorrectmatrix + owner: bgruening + revisions: + - ea19190ce5e0 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hiccorrelate + owner: bgruening + revisions: + - 2b4d6a8dab36 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicdetectloops + owner: bgruening + revisions: + - 0410b6aada45 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicdifferentialtad + owner: bgruening + revisions: + - 77d8e0fd162a + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicfindrestrictionsites + owner: bgruening + revisions: + - 6c5097f6d41e + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicfindtads + owner: bgruening + revisions: + - ec4b948dc6f0 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hichyperoptdetectloops + owner: bgruening + revisions: + - 7f7c6ead2d0d + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicinfo + owner: bgruening + revisions: + - e4f8fceab96a + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicinterintratad + owner: bgruening + revisions: + - 55b013e59018 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicmergedomains + owner: bgruening + revisions: + - b376ef118807 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicmergeloops + owner: bgruening + revisions: + - 1511a8ebe906 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicmergematrixbins + owner: bgruening + revisions: + - 977dc15add20 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicnormalize + owner: bgruening + revisions: + - 6d042c96aceb + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicpca + owner: bgruening + revisions: + - 77919cc3618e + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicplotaverageregions + owner: bgruening + revisions: + - ea5d67ec94ab + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicplotdistvscounts + owner: bgruening + revisions: + - 6326cd29c1c3 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicplotmatrix + owner: bgruening + revisions: + - b63363075c2e + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicplotsvl + owner: bgruening + revisions: + - b4e780e93c91 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicplotviewpoint + owner: bgruening + revisions: + - 58de3c7c8e89 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicquickqc + owner: bgruening + revisions: + - 21d859ad4502 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicsummatrices + owner: bgruening + revisions: + - 36dfa2825a59 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hictadclassifier + owner: bgruening + revisions: + - 887d203233e5 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hictraintadclassifier + owner: bgruening + revisions: + - 1ff19476c5a5 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hictransform + owner: bgruening + revisions: + - f36828ebdc54 + tool_panel_section_label: Single-Cell +- name: hicexplorer_hicvalidatelocations + owner: bgruening + revisions: + - 1d201e8378b3 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicadjustmatrix + owner: iuc + revisions: + - 2e773e00ceb0 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schiccluster + owner: iuc + revisions: + - baa3ae7ac42c + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicclustercompartments + owner: iuc + revisions: + - 54b6cef88a7f + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicclusterminhash + owner: iuc + revisions: + - 3048283ee054 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicclustersvl + owner: iuc + revisions: + - e6ec3914a076 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicconsensusmatrices + owner: iuc + revisions: + - 33b1c99cc709 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schiccorrectmatrices + owner: iuc + revisions: + - 295558e266d0 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schiccreatebulkmatrix + owner: iuc + revisions: + - acb3ed49109e + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicdemultiplex + owner: iuc + revisions: + - f224fc9af1d3 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicinfo + owner: iuc + revisions: + - 41b415c410e3 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicmergematrixbins + owner: iuc + revisions: + - 47ef02546fe9 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicmergetoscool + owner: iuc + revisions: + - 70a13d0a950f + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicnormalize + owner: iuc + revisions: + - 66e96c3d3c5d + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicplotclusterprofiles + owner: iuc + revisions: + - 65f2f5d29947 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicplotconsensusmatrices + owner: iuc + revisions: + - 95b1216e1e70 + tool_panel_section_label: Single-Cell +- name: schicexplorer_schicqualitycontrol + owner: iuc + revisions: + - 4a841ab67e3b + tool_panel_section_label: Single-Cell +- name: quantification + owner: perssond + revisions: + - 3a916c4e9f5f + tool_panel_section_label: Single-Cell +- name: cell_intensity_processing + owner: goeckslab + revisions: + - 5d541df02496 + tool_panel_section_label: Single-Cell +- name: s3segmenter + owner: perssond + revisions: + - 96d0d969ebc9 + tool_panel_section_label: Single-Cell +- name: slice_image + owner: imgteam + revisions: + - a72590196440 + tool_panel_section_label: Single-Cell +- name: squidpy + owner: goeckslab + revisions: + - d30ef0613122 + tool_panel_section_label: Single-Cell +- name: vitessce_spatial + owner: goeckslab + revisions: + - 7cc457aa78b1 + tool_panel_section_label: Single-Cell +- name: run_sccaf + owner: ebi-gxa + revisions: + - 647d34f125bc + tool_panel_section_label: Single-Cell +- name: sccaf_asses + owner: ebi-gxa + revisions: + - 37a4c22f600b + tool_panel_section_label: Single-Cell +- name: sccaf_asses_merger + owner: ebi-gxa + revisions: + - 99d15ded4d5f + tool_panel_section_label: Single-Cell +- name: sccaf_regress_out + owner: ebi-gxa + revisions: + - 5ef0610e9f50 + tool_panel_section_label: Single-Cell +- name: episcanpy_cluster_embed + owner: iuc + revisions: + - f4713992f23a + tool_panel_section_label: Single-Cell +- name: 10x_bamtofastq + owner: bgruening + revisions: + - f71fd828c126 + tool_panel_section_label: Single-Cell +- name: scater_read_10x_results + owner: ebi-gxa + revisions: + - da3f394039b5 + tool_panel_section_label: Single-Cell +- name: gsc_scran_normalize + owner: artbio + revisions: + - 6864acb21714 + tool_panel_section_label: Single-Cell +- name: seurat_create_seurat_object + owner: ebi-gxa + revisions: + - f8865ae30723 + tool_panel_section_label: Single-Cell +- name: seurat_export_cellbrowser + owner: ebi-gxa + revisions: + - 36221da750e8 + tool_panel_section_label: Single-Cell +- name: seurat_filter_cells + owner: ebi-gxa + revisions: + - cd9f564bd63f + tool_panel_section_label: Single-Cell +- name: seurat_find_clusters + owner: ebi-gxa + revisions: + - d541e9e62beb + tool_panel_section_label: Single-Cell +- name: seurat_find_markers + owner: ebi-gxa + revisions: + - 07fc9f4841b3 + tool_panel_section_label: Single-Cell +- name: seurat_find_neighbours + owner: ebi-gxa + revisions: + - ba897c57bdd9 + tool_panel_section_label: Single-Cell +- name: seurat_find_variable_genes + owner: ebi-gxa + revisions: + - 948fc0276b4f + tool_panel_section_label: Single-Cell +- name: seurat_normalise_data + owner: ebi-gxa + revisions: + - 3f49bc9c9213 + tool_panel_section_label: Single-Cell +- name: seurat_dim_plot + owner: ebi-gxa + revisions: + - 64174ac50d78 + tool_panel_section_label: Single-Cell +- name: seurat_read10x + owner: ebi-gxa + revisions: + - f5db0e853f57 + tool_panel_section_label: Single-Cell +- name: seurat_run_pca + owner: ebi-gxa + revisions: + - 8ded486b0014 + tool_panel_section_label: Single-Cell +- name: seurat_run_tsne + owner: ebi-gxa + revisions: + - 0db997e4a81d + tool_panel_section_label: Single-Cell +- name: seurat_scale_data + owner: ebi-gxa + revisions: + - 5e9ba303f9e1 + tool_panel_section_label: Single-Cell diff --git a/communities/microgalaxy/lab/usegalaxy.eu.yml b/communities/microgalaxy/lab/usegalaxy.eu.yml new file mode 100644 index 00000000..67143644 --- /dev/null +++ b/communities/microgalaxy/lab/usegalaxy.eu.yml @@ -0,0 +1,55 @@ +# This content extends base.yml + +# Request this as a webpage with: +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/usegalaxy.eu.yml + +# ----------------------------------------------------------------------------- +# Use these variables in HTML templates like: +# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}" +# To make the content more generic and reusable across sites + +# These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!" +site_name: Europe +nationality: European + +# Used for rendering tool/workflow links. Trailing '/' will be removed. +galaxy_base_url: https://singlecell.usegalaxy.eu +subdomain: singlecell +root_domain: usegalaxy.eu + +# This will enable a feedback form on the webpage: +# feedback_email: help@mygalaxy.org + +quota_request_url: https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform +data_policy_url: "#data-policy" +terms_url: https://usegalaxy-eu.github.io/gdpr/tos.html + +help_links: + - title: Single Cell community help forum + url: https://help.galaxyproject.org/tag/scrna + - title: General Galaxy support + url: https://galaxyproject.org/support/ + - title: Galaxy EU help forum + url: https://help.galaxyproject.org/c/usegalaxy-eu-support/6 + - title: Single cell Galaxy user community chat room + url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - title: Galaxy Training Community chat + url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im + - title: Usegalaxy.eu chat + url: https://matrix.to/#/#usegalaxy-eu_Lobby:gitter.im + - title: Usegalaxy.org chat + url: https://matrix.to/#/#galaxyproject_Lobby:gitter.im + +conclusion_extra_md: > +
+ {% markdown_from_url 'https://raw.githubusercontent.com/galaxyproject/galaxy-hub/master/content/eu/common/data-policy.md' %} +
+
+ +
+ +# ----------------------------------------------------------------------------- +# Custom content relative to this file URL + +custom_css: usegalaxy.eu/static/custom.css +footer_md: usegalaxy.eu/templates/footer.html diff --git a/communities/microgalaxy/lab/usegalaxy.eu/static/custom.css b/communities/microgalaxy/lab/usegalaxy.eu/static/custom.css new file mode 100644 index 00000000..a579d07b --- /dev/null +++ b/communities/microgalaxy/lab/usegalaxy.eu/static/custom.css @@ -0,0 +1,10 @@ +#conclusionExtra h1 { + font-size: 1.5rem; + margin-bottom: 1rem; +} +#conclusionExtra { + font-size: 90%; +} +#conclusionExtra td { + font-size: 90%; +} \ No newline at end of file diff --git a/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html new file mode 100644 index 00000000..0ff9c101 --- /dev/null +++ b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html @@ -0,0 +1,70 @@ + diff --git a/communities/microgalaxy/lab/usegalaxy.org.au.yml b/communities/microgalaxy/lab/usegalaxy.org.au.yml new file mode 100644 index 00000000..0a032cc7 --- /dev/null +++ b/communities/microgalaxy/lab/usegalaxy.org.au.yml @@ -0,0 +1,43 @@ +# This content extends base.yml + +# Request this as a webpage with: +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/usegalaxy.org.au.yml + +# ----------------------------------------------------------------------------- +# Use these variables in MD/HTML templates like: +# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}" +# To make the content more generic and reusable across sites + +# These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!" +site_name: Australia +nationality: Australian + +# Used for rendering tool/workflow links. Trailing '/' will be removed. +galaxy_base_url: https://singlecell.usegalaxy.org.au +subdomain: singlecell +root_domain: usegalaxy.org.au + +# This will enable a feedback form on the webpage: +feedback_email: help@genome.edu.au + +# More variables for MD/HTML templating +support_url: https://site.usegalaxy.org.au/request +quota_request_url: https://site.usegalaxy.org.au/request/quota +data_policy_url: https://site.usegalaxy.org.au/about#data-privacy +terms_url: https://site.usegalaxy.org.au/about#terms-of-service + +help_links: + - title: Galaxy Australia Support + url: https://site.usegalaxy.org.au/request + - title: General Galaxy support + url: https://galaxyproject.org/support/ + - title: Single Cell community help forum + url: https://usegalaxy-eu.github.io/scrna + - title: General Galaxy help forum + url: https://help.galaxyproject.org + - title: Single cell Galaxy user community chat room + url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - title: Galaxy Training Community chat + url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im + - title: Usegalaxy.org chat + url: https://matrix.to/#/#galaxyproject_Lobby:gitter.im diff --git a/communities/microgalaxy/lab/usegalaxy.org.au/templates/footer.html b/communities/microgalaxy/lab/usegalaxy.org.au/templates/footer.html new file mode 100644 index 00000000..fa4d580e --- /dev/null +++ b/communities/microgalaxy/lab/usegalaxy.org.au/templates/footer.html @@ -0,0 +1,119 @@ + diff --git a/communities/microgalaxy/lab/usegalaxy.org.yml b/communities/microgalaxy/lab/usegalaxy.org.yml new file mode 100644 index 00000000..63934752 --- /dev/null +++ b/communities/microgalaxy/lab/usegalaxy.org.yml @@ -0,0 +1,35 @@ +# This content extends base.yml + +# Request this as a webpage with: +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/usegalaxy.org.yml + +# ----------------------------------------------------------------------------- +# Use these variables in HTML templates like: +# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}" +# To make the content more generic and reusable across sites + +# These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!" +site_name: "" # ? +nationality: "" + +# Used for rendering tool/workflow links. Trailing '/' will be removed. +galaxy_base_url: https://singlecell.usegalaxy.org +subdomain: singlecell +root_domain: usegalaxy.org + +# This will enable a feedback form on the webpage: +# feedback_email: help@mygalaxy.org + +help_links: + - title: Single Cell community help forum + url: https://usegalaxy-eu.github.io/scrna + - title: General Galaxy support + url: https://galaxyproject.org/support/ + - title: General Galaxy help forum + url: https://help.galaxyproject.org + - title: Single cell Galaxy user community chat room + url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - title: Galaxy Training Community chat + url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im + - title: Usegalaxy.org chat + url: https://matrix.to/#/#galaxyproject_Lobby:gitter.im From b0c28f0bcc06d9c67a6b30d98e4bb1c539547895 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 12:11:23 +0100 Subject: [PATCH 02/38] tool list --- communities/microgalaxy/lab/sections/5_tools.yml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 communities/microgalaxy/lab/sections/5_tools.yml diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml new file mode 100644 index 00000000..6091bc12 --- /dev/null +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -0,0 +1,9 @@ +id: tools +title: Community Tools +tabs: + - id: tool_list + title: List of community curated tools available for microGalaxy + content: + - title_md: Tool A + description_md: > + Tools bla From dca27f32fe762f31e4cd6b27f3a5a6081a196c1b Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 12:12:16 +0100 Subject: [PATCH 03/38] tool list --- communities/microgalaxy/lab/base.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index d9fec4da..f48401be 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -64,5 +64,6 @@ sections: - sections/1_beginner.yml - sections/3_advanced.yml - sections/4_community.yml + - sections/5_tools.yml # ----------------------------------------------------------------------------- From ca61179487eae196727ec377b2972d2c412edfe3 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 12:20:52 +0100 Subject: [PATCH 04/38] add link --- communities/microgalaxy/lab/sections/5_tools.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 6091bc12..33ad5a1b 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -6,4 +6,4 @@ tabs: content: - title_md: Tool A description_md: > - Tools bla + [Tool link]({{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fdropletutils_read_10x%2fdropletutils_read_10x) From bdfc5a5d0ca10d8f97b0c8f13b130d4a53bd4e24 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 14:13:57 +0100 Subject: [PATCH 05/38] multiple tools --- communities/microgalaxy/lab/sections/5_tools.yml | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 33ad5a1b..3c605ceb 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -6,4 +6,14 @@ tabs: content: - title_md: Tool A description_md: > - [Tool link]({{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fdropletutils_read_10x%2fdropletutils_read_10x) + * Galaxy tool ids 1 + * Description 1 + - title_md: Tool B + description_md: > + * Galaxy tool ids 1 + * Description 1 + - title_md: Tool C + description_md: > + * Galaxy tool ids 1 + * Description 1 + From 9e4faeea27e12ddbd11ffa7415eef5bdaef4fdeb Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 14:16:34 +0100 Subject: [PATCH 06/38] multiple tools --- communities/microgalaxy/lab/sections/5_tools.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 3c605ceb..26c73959 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -6,14 +6,14 @@ tabs: content: - title_md: Tool A description_md: > - * Galaxy tool ids 1 - * Description 1 + - Galaxy tool ids 1 + - Description 1 - title_md: Tool B description_md: > - * Galaxy tool ids 1 - * Description 1 + - Galaxy tool ids 1 + - Description 1 - title_md: Tool C description_md: > - * Galaxy tool ids 1 - * Description 1 + - Galaxy tool ids 1 + - Description 1 From b4558f7ab6797e445a3cf874006f3b0485adba43 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 14:20:58 +0100 Subject: [PATCH 07/38] multiple tools --- communities/microgalaxy/lab/sections/5_tools.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 26c73959..b50b956a 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -6,14 +6,14 @@ tabs: content: - title_md: Tool A description_md: > - - Galaxy tool ids 1 - - Description 1 + - Galaxy tool ids 1 + - Description 1 - title_md: Tool B description_md: > - - Galaxy tool ids 1 - - Description 1 + - Galaxy tool ids 1 + - Description 1 - title_md: Tool C description_md: > - - Galaxy tool ids 1 - - Description 1 + - Galaxy tool ids 1 + - Description 1 From 9722b4c4d165f7ead8197b3c057729a3b20f63c9 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 14:22:56 +0100 Subject: [PATCH 08/38] multiple tools --- communities/microgalaxy/lab/sections/5_tools.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index b50b956a..5e87e250 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -6,14 +6,14 @@ tabs: content: - title_md: Tool A description_md: > - - Galaxy tool ids 1 - - Description 1 + * Galaxy tool ids 1 + * Description 1 - title_md: Tool B description_md: > - - Galaxy tool ids 1 - - Description 1 + * Galaxy tool ids 1 + * Description 1 - title_md: Tool C description_md: > - - Galaxy tool ids 1 - - Description 1 + * Galaxy tool ids 1 + * Description 1 From 66294a41087ab8fc00e3f83c4fd714627bd5bb84 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 14:26:50 +0100 Subject: [PATCH 09/38] multiple tools --- .../microgalaxy/lab/sections/5_tools.yml | 23 +++++++++++-------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 5e87e250..b8c371e5 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -2,18 +2,23 @@ id: tools title: Community Tools tabs: - id: tool_list - title: List of community curated tools available for microGalaxy + title: List of community curated tools available for microGalaxy content: - title_md: Tool A - description_md: > + description_md: | + """ * Galaxy tool ids 1 * Description 1 + """ - title_md: Tool B - description_md: > - * Galaxy tool ids 1 - * Description 1 + description_md: | + """ + * Galaxy tool ids 2 + * Description 2 + """ - title_md: Tool C - description_md: > - * Galaxy tool ids 1 - * Description 1 - + description_md: | + """ + * Galaxy tool ids 3 + * Description 3 + """ \ No newline at end of file From 6ee3ea1dd59a5d4d38ae3abcdd8dca223d7b9f37 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 14:29:15 +0100 Subject: [PATCH 10/38] multiple tools --- .../microgalaxy/lab/sections/5_tools.yml | 39 +++++++++++++------ 1 file changed, 27 insertions(+), 12 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index b8c371e5..f32f15a4 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -6,19 +6,34 @@ tabs: content: - title_md: Tool A description_md: | - """ - * Galaxy tool ids 1 - * Description 1 - """ +
    +
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • +
  • data interoperability
    • +
  • bacteria
    • +
  • prokaryote
    • +
  • microbiome
    • +
  • micro-organism
    • +
  • pathogen
    • +
- title_md: Tool B description_md: | - """ - * Galaxy tool ids 2 - * Description 2 - """ +
    +
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • +
  • data interoperability
    • +
  • bacteria
    • +
  • prokaryote
    • +
  • microbiome
    • +
  • micro-organism
    • +
  • pathogen
    • +
- title_md: Tool C description_md: | - """ - * Galaxy tool ids 3 - * Description 3 - """ \ No newline at end of file +
    +
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • +
  • data interoperability
    • +
  • bacteria
    • +
  • prokaryote
    • +
  • microbiome
    • +
  • micro-organism
    • +
  • pathogen
    • +
\ No newline at end of file From fdb5f0ce9667ddf5c710560b3d60b50227a073a5 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 14:44:31 +0100 Subject: [PATCH 11/38] multiple tools --- .../microgalaxy/lab/sections/5_tools.yml | 16436 +++++++++++++++- 1 file changed, 16399 insertions(+), 37 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index f32f15a4..31f1980c 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -1,39 +1,16401 @@ id: tools -title: Community Tools tabs: - - id: tool_list - title: List of community curated tools available for microGalaxy - content: - - title_md: Tool A - description_md: | -
    -
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • -
  • data interoperability
    • -
  • bacteria
    • -
  • prokaryote
    • -
  • microbiome
    • -
  • micro-organism
    • -
  • pathogen
    • -
- - title_md: Tool B - description_md: | -
    -
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • -
  • data interoperability
    • -
  • bacteria
    • -
  • prokaryote
    • -
  • microbiome
    • -
  • micro-organism
    • -
  • pathogen
    • -
- - title_md: Tool C - description_md: | -
    -
  • training (for workflows that correspond to the Galaxy Training Network's tutorials)
    • -
  • data interoperability
    • -
  • bacteria
    • -
  • prokaryote
    • -
  • microbiome
    • -
  • micro-organism
    • -
  • pathogen
    • -
\ No newline at end of file +- content: + - description_md: '
  • Galaxy tool ids: pampa_communitymetrics, + pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm
  • Description: + Tools to compute and analyse biodiversity metrics
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: nan
  • ToolShed categories: + Ecology
  • ToolShed id: pampa
  • Date of first + commit of the suite: 2020-11-13
  • Galaxy wrapper owner: + ecology
  • Galaxy wrapper source: https://github.com/ColineRoyaux/PAMPA-Galaxy
  • Galaxy + wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA
  • Galaxy + wrapper version: 0.0.2
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 5
  • Available + on UseGalaxy.eu: 5
  • Available on UseGalaxy.fr: 5
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 5
  • Tools available on UseGalaxy.eu: + 5
  • Tools available on UseGalaxy.fr: 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: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + 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.no: 4
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1038
  • No. of tool users (all time) (usegalaxy.eu): 1038
  • Tool + usage (5 years) (usegalaxy.eu): 146
  • Tool usage (all time) + (usegalaxy.eu): 146
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 849
  • No. of tool users (all time) (usegalaxy.org.au): 849
  • Tool + usage (5 years) (usegalaxy.org.au): 38
  • Tool usage (all + time) (usegalaxy.org.au): 38
  • No. of tool users (5 years) + - all main servers: 1887
  • No. of tool users (all time) - + all main servers: 1887
  • Tool usage (5 years) - all main + servers: 184
  • Tool usage (all time) - all main servers: + 184
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: PAMPA + - description_md: '
  • Galaxy tool ids: treebest_best
  • Description: + TreeBeST best
  • bio.tool id: treebest
  • bio.tool + ids: treebest
  • biii: nan
  • bio.tool name: + TreeBeST
  • 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.
  • EDAM + operation: Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic + inference (from molecular sequences)
  • EDAM topic: Phylogenetics
  • Status: + To update
  • Source: http://treesoft.sourceforge.net/treebest.shtml
  • ToolShed + categories: Phylogenetics
  • ToolShed id: treebest_best
  • Date + of first commit of the suite: 2015-08-06
  • Galaxy wrapper + owner: earlhaminst
  • Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest
  • Galaxy + wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest
  • Galaxy + wrapper version: 1.9.2.post0
  • Conda id: treebest
  • Conda + version: 1.9.2.post1
  • EDAM operation (no superclasses): + Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)
  • EDAM + topic (no superclasses): Phylogenetics
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1003
  • No. of tool users (all time) (usegalaxy.eu): 1022
  • Tool + usage (5 years) (usegalaxy.eu): 48
  • Tool usage (all time) + (usegalaxy.eu): 52
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 1003
  • No. of tool users (all time) - all main + servers: 1022
  • Tool usage (5 years) - all main servers: + 48
  • Tool usage (all time) - all main servers: 52
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: TreeBest + - description_md: '
  • Galaxy tool ids: abacas
  • Description: + Order and Orientate Contigs
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://github.com/phac-nml/abacas
  • ToolShed categories: + Assembly
  • ToolShed id: abacas
  • Date of first + commit of the suite: 2019-11-20
  • Galaxy wrapper owner: + nml
  • Galaxy wrapper source: https://github.com/phac-nml/abacas
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas
  • Galaxy + wrapper version: 1.1
  • Conda id: mummer
  • Conda + version: 3.23
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: abacas + - description_md: '
  • Galaxy tool ids: abricate, abricate_list, + abricate_summary
  • Description: Mass screening of contigs + for antiobiotic resistance genes
  • bio.tool id: ABRicate
  • bio.tool + ids: ABRicate
  • biii: nan
  • bio.tool name: + ABRicate
  • bio.tool description: Mass screening of contigs + for antimicrobial resistance or virulence genes.
  • EDAM operation: + Antimicrobial resistance prediction
  • EDAM topic: Genomics, + Microbiology
  • Status: Up-to-date
  • Source: + https://github.com/tseemann/abricate
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: abricate
  • Date + of first commit of the suite: 2017-07-10
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate
  • Galaxy + wrapper version: 1.0.1
  • Conda id: abricate
  • Conda + version: 1.0.1
  • EDAM operation (no superclasses): + Antimicrobial resistance prediction
  • EDAM topic (no superclasses): + Genomics, Microbiology
  • Available on UseGalaxy.org (Main): + 3
  • Available on UseGalaxy.org.au: 3
  • Available + on UseGalaxy.eu: 3
  • Available on UseGalaxy.fr: 3
  • Tools + available on UseGalaxy.org (Main): 3
  • Tools available on + UseGalaxy.org.au: 3
  • Tools available on UseGalaxy.eu: + 3
  • Tools available on UseGalaxy.fr: 3
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 619817
  • No. of tool users (all time) (usegalaxy.eu): 622353
  • Tool + usage (5 years) (usegalaxy.eu): 4097
  • Tool usage (all time) + (usegalaxy.eu): 4130
  • No. of tool users (5 years) (usegalaxy.org): + 320454
  • No. of tool users (all time) (usegalaxy.org): 320454
  • Tool + usage (5 years) (usegalaxy.org): 2915
  • Tool usage (all time) + (usegalaxy.org): 2915
  • No. of tool users (5 years) (usegalaxy.org.au): + 496156
  • No. of tool users (all time) (usegalaxy.org.au): + 503743
  • Tool usage (5 years) (usegalaxy.org.au): 2012
  • Tool + usage (all time) (usegalaxy.org.au): 2227
  • No. of tool users + (5 years) - all main servers: 1436427
  • No. of tool users + (all time) - all main servers: 1446550
  • Tool usage (5 years) + - all main servers: 9024
  • Tool usage (all time) - all main + servers: 9272
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: abricate + - description_md: '
  • Galaxy tool ids: abritamr
  • Description: + A pipeline for running AMRfinderPlus and collating results into functional classes
  • bio.tool + id: abritamr
  • bio.tool ids: abritamr
  • biii: + nan
  • bio.tool name: abriTAMR
  • 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.
  • EDAM operation: + Antimicrobial resistance prediction
  • EDAM topic: Microbiology, + Public health and epidemiology, Infectious disease
  • Status: + Up-to-date
  • Source: https://zenodo.org/record/7370628
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: abritamr
  • Date + of first commit of the suite: 2023-04-03
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr
  • Galaxy + wrapper version: 1.0.19
  • Conda id: abritamr
  • Conda + version: 1.0.19
  • EDAM operation (no superclasses): + Antimicrobial resistance prediction
  • EDAM topic (no superclasses): + Microbiology, Public health and epidemiology, Infectious disease
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1139
  • No. of tool + users (all time) (usegalaxy.eu): 1139
  • Tool usage (5 years) + (usegalaxy.eu): 109
  • Tool usage (all time) (usegalaxy.eu): + 109
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1139
  • No. + of tool users (all time) - all main servers: 1139
  • Tool + usage (5 years) - all main servers: 109
  • Tool usage (all + time) - all main servers: 109
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: abritamr + - description_md: '
  • Galaxy tool ids: abyss-pe
  • Description: + Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
  • bio.tool + id: abyss
  • bio.tool ids: abyss
  • biii: + nan
  • bio.tool name: ABySS
  • bio.tool description: + De novo genome sequence assembler using short reads.
  • EDAM operation: + Genome assembly, De-novo assembly, Scaffolding
  • EDAM topic: + Sequence assembly
  • Status: Up-to-date
  • Source: + http://www.bcgsc.ca/platform/bioinfo/software/abyss
  • ToolShed categories: + Assembly
  • ToolShed id: abyss
  • Date of first + commit of the suite: 2015-04-14
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss
  • Galaxy + wrapper version: 2.3.9
  • Conda id: abyss
  • Conda + version: 2.3.9
  • EDAM operation (no superclasses): + Genome assembly, De-novo assembly, Scaffolding
  • EDAM topic (no + superclasses): Sequence assembly
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 5543
  • No. of tool users (all time) (usegalaxy.eu): 5543
  • Tool + usage (5 years) (usegalaxy.eu): 1042
  • Tool usage (all time) + (usegalaxy.eu): 1042
  • No. of tool users (5 years) (usegalaxy.org): + 1301
  • No. of tool users (all time) (usegalaxy.org): 1305
  • Tool + usage (5 years) (usegalaxy.org): 413
  • Tool usage (all time) + (usegalaxy.org): 414
  • No. of tool users (5 years) (usegalaxy.org.au): + 2030
  • No. of tool users (all time) (usegalaxy.org.au): 2030
  • Tool + usage (5 years) (usegalaxy.org.au): 299
  • Tool usage (all + time) (usegalaxy.org.au): 299
  • No. of tool users (5 years) + - all main servers: 8874
  • No. of tool users (all time) - + all main servers: 8878
  • Tool usage (5 years) - all main + servers: 1754
  • Tool usage (all time) - all main servers: + 1755
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: abyss + - description_md: '
  • Galaxy tool ids: aldex2
  • Description: + Performs analysis Of differential abundance taking sample variation into account
  • bio.tool + id: aldex2
  • bio.tool ids: aldex2
  • biii: + nan
  • bio.tool name: ALDEx2
  • 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.
  • EDAM + operation: Statistical inference
  • EDAM topic: Gene + expression, Statistics and probability
  • Status: To update
  • Source: + https://github.com/ggloor/ALDEx_bioc
  • ToolShed categories: + Metagenomics
  • ToolShed id: aldex2
  • Date of + first commit of the suite: 2022-06-29
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2
  • Galaxy + wrapper version: 1.26.0
  • Conda id: bioconductor-aldex2
  • Conda + version: 1.34.0
  • EDAM operation (no superclasses): + Statistical inference
  • EDAM topic (no superclasses): Gene + expression, Statistics and probability
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 262
  • No. of tool users (all time) (usegalaxy.eu): 262
  • Tool + usage (5 years) (usegalaxy.eu): 36
  • Tool usage (all time) + (usegalaxy.eu): 36
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 262
  • No. of tool users (all time) - all main + servers: 262
  • Tool usage (5 years) - all main servers: + 36
  • Tool usage (all time) - all main servers: 36
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: aldex2 + - description_md: '
  • Galaxy tool ids: amplican
  • Description: + AmpliCan is an analysis tool for genome editing.
  • bio.tool id: + amplican
  • bio.tool ids: amplican
  • biii: + nan
  • bio.tool name: amplican
  • 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.
  • EDAM operation: Alignment, Standardisation + and normalisation
  • EDAM topic: PCR experiment, Statistics + and probability
  • Status: To update
  • Source: + https://github.com/valenlab/amplican
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: amplican
  • Date + of first commit of the suite: 2021-09-22
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican
  • Galaxy + wrapper version: 1.14.0
  • Conda id: bioconductor-amplican
  • Conda + version: 1.24.0
  • EDAM operation (no superclasses): + Alignment, Standardisation and normalisation
  • EDAM topic (no superclasses): + PCR experiment, Statistics and probability
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 81
  • No. of tool users (all time) (usegalaxy.eu): 81
  • Tool + usage (5 years) (usegalaxy.eu): 17
  • Tool usage (all time) + (usegalaxy.eu): 17
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 81
  • No. of tool users (all time) - all main + servers: 81
  • Tool usage (5 years) - all main servers: + 17
  • Tool usage (all time) - all main servers: 17
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: amplican + - description_md: '
  • Galaxy tool ids: amrfinderplus
  • 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
  • biii: nan
  • bio.tool + name: AMRFinderPlus
  • 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
  • EDAM + operation: Antimicrobial resistance prediction
  • EDAM topic: + Microbiology, Public health and epidemiology, Infectious disease
  • Status: + Up-to-date
  • Source: https://github.com/ncbi/amr
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: AMRFinderPlus
  • Date + of first commit of the suite: 2023-05-12
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus
  • Galaxy + wrapper version: 3.12.8
  • Conda id: ncbi-amrfinderplus
  • Conda + version: 3.12.8
  • EDAM operation (no superclasses): + Antimicrobial resistance prediction
  • EDAM topic (no superclasses): + Microbiology, Public health and epidemiology, Infectious disease
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 5734
  • No. of tool + users (all time) (usegalaxy.eu): 5734
  • Tool usage (5 years) + (usegalaxy.eu): 334
  • Tool usage (all time) (usegalaxy.eu): + 334
  • No. of tool users (5 years) (usegalaxy.org): 1035
  • No. + of tool users (all time) (usegalaxy.org): 1035
  • Tool usage + (5 years) (usegalaxy.org): 106
  • Tool usage (all time) (usegalaxy.org): + 106
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 6769
  • No. + of tool users (all time) - all main servers: 6769
  • Tool + usage (5 years) - all main servers: 440
  • Tool usage (all + time) - all main servers: 440
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: amrfinderplus + - description_md: '
  • Galaxy tool ids: ancombc
  • Description: + Performs analysis of compositions of microbiomes with bias correction.
  • bio.tool + id: ancombc
  • bio.tool ids: ancombc
  • biii: + nan
  • bio.tool name: ANCOMBC
  • 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.
  • EDAM operation: + DNA barcoding
  • EDAM topic: Microbial ecology, Metagenomics, + Taxonomy
  • Status: To update
  • Source: + https://github.com/FrederickHuangLin/ANCOMBC
  • ToolShed categories: + Metagenomics
  • ToolShed id: ancombc
  • Date of + first commit of the suite: 2022-07-16
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc
  • Galaxy + wrapper version: 1.4.0
  • Conda id: bioconductor-ancombc
  • Conda + version: 2.4.0
  • EDAM operation (no superclasses): + DNA barcoding
  • EDAM topic (no superclasses): Microbial ecology, + Metagenomics, Taxonomy
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 26
  • No. of tool users (all time) (usegalaxy.eu): 26
  • Tool + usage (5 years) (usegalaxy.eu): 7
  • Tool usage (all time) + (usegalaxy.eu): 7
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 26
  • No. of tool users (all time) - all main + servers: 26
  • Tool usage (5 years) - all main servers: + 7
  • Tool usage (all time) - all main servers: 7
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: ancombc + - description_md: '
  • Galaxy tool ids: antismash
  • Description: + Antismash allows the genome-wide identification, annotation and analysis of + secondary metabolite biosynthesis gene clusters
  • bio.tool id: + antismash
  • bio.tool ids: antismash
  • biii: + nan
  • bio.tool name: antiSMASH
  • bio.tool description: + Rapid 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.
  • EDAM operation: Sequence + clustering, Gene prediction, Differential gene expression analysis
  • EDAM + topic: Molecular interactions, pathways and networks, Gene and protein + families
  • Status: To update
  • Source: + https://antismash.secondarymetabolites.org
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: antismash
  • Date + of first commit of the suite: 2015-02-28
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/antismash
  • Galaxy + wrapper version: 6.1.1
  • Conda id: antismash
  • Conda + version: 7.1.0
  • EDAM operation (no superclasses): + Sequence clustering, Gene prediction, Differential gene expression analysis
  • EDAM + topic (no superclasses): Molecular interactions, pathways and networks, + Gene and protein families
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 15949
  • No. of tool users (all time) (usegalaxy.eu): 16490
  • Tool + usage (5 years) (usegalaxy.eu): 726
  • Tool usage (all time) + (usegalaxy.eu): 811
  • No. of tool users (5 years) (usegalaxy.org): + 5113
  • No. of tool users (all time) (usegalaxy.org): 5113
  • Tool + usage (5 years) (usegalaxy.org): 649
  • Tool usage (all time) + (usegalaxy.org): 649
  • No. of tool users (5 years) (usegalaxy.org.au): + 6043
  • No. of tool users (all time) (usegalaxy.org.au): 6043
  • Tool + usage (5 years) (usegalaxy.org.au): 169
  • Tool usage (all + time) (usegalaxy.org.au): 169
  • No. of tool users (5 years) + - all main servers: 27105
  • No. of tool users (all time) + - all main servers: 27646
  • Tool usage (5 years) - all main + servers: 1544
  • Tool usage (all time) - all main servers: + 1629
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: antismash + - description_md: '
  • Galaxy tool ids: artic_guppyplex, artic_minion
  • 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
  • bio.tool id: artic
  • bio.tool ids: + artic
  • biii: nan
  • bio.tool name: ARTIC
  • bio.tool + description: A bioinformatics pipeline for working with virus sequencing + data sequenced with nanopore
  • EDAM operation: Sequence alignment
  • EDAM + topic: Genomics
  • Status: To update
  • Source: + https://github.com/artic-network/fieldbioinformatics
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: nan
  • Date + of first commit of the suite: 2020-04-22
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic
  • Galaxy + wrapper version: nan
  • Conda id: artic
  • Conda + version: 1.2.4
  • EDAM operation (no superclasses): + Sequence alignment
  • EDAM topic (no superclasses): Genomics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 2
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 2
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 9021
  • No. of tool + users (all time) (usegalaxy.eu): 9021
  • Tool usage (5 years) + (usegalaxy.eu): 238
  • Tool usage (all time) (usegalaxy.eu): + 238
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 9021
  • No. + of tool users (all time) - all main servers: 9021
  • Tool + usage (5 years) - all main servers: 238
  • Tool usage (all + time) - all main servers: 238
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: artic + - description_md: '
  • Galaxy tool ids: assemblystats
  • Description: + Summarise an assembly (e.g. N50 metrics)
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://github.com/phac-nml/galaxy_tools
  • ToolShed categories: + Assembly
  • ToolShed id: assemblystats
  • Date + of first commit of the suite: 2017-10-13
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats
  • Galaxy + wrapper version: 1.1.0
  • Conda id: perl-bioperl
  • Conda + version: 1.7.8
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: assemblystats + - description_md: '
  • Galaxy tool ids: bakta
  • 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."
  • bio.tool id: bakta
  • bio.tool + ids: bakta
  • biii: nan
  • bio.tool name: + Bakta
  • bio.tool description: Rapid & standardized annotation + of bacterial genomes, MAGs & plasmids
  • EDAM operation: Genome + annotation
  • EDAM topic: Genomics, Data submission, annotation + and curation, Sequence analysis
  • Status: Up-to-date
  • Source: + https://github.com/oschwengers/bakta
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: bakta
  • Date + of first commit of the suite: 2022-09-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta
  • Galaxy + wrapper version: 1.9.4
  • Conda id: bakta
  • Conda + version: 1.9.4
  • EDAM operation (no superclasses): + Genome annotation
  • EDAM topic (no superclasses): Genomics, + Data submission, annotation and curation, Sequence analysis
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 11117
  • No. of tool + users (all time) (usegalaxy.eu): 11117
  • Tool usage (5 years) + (usegalaxy.eu): 534
  • Tool usage (all time) (usegalaxy.eu): + 534
  • No. of tool users (5 years) (usegalaxy.org): 19
  • No. + of tool users (all time) (usegalaxy.org): 19
  • Tool usage + (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): + 1
  • No. of tool users (5 years) (usegalaxy.org.au): 9601
  • No. + of tool users (all time) (usegalaxy.org.au): 9601
  • Tool + usage (5 years) (usegalaxy.org.au): 167
  • Tool usage (all + time) (usegalaxy.org.au): 167
  • No. of tool users (5 years) + - all main servers: 20737
  • No. of tool users (all time) + - all main servers: 20737
  • Tool usage (5 years) - all main + servers: 702
  • Tool usage (all time) - all main servers: + 702
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: bakta + - description_md: '
  • Galaxy tool ids: bamtools
  • Description: + Operate on and transform BAM datasets in various ways using bamtools
  • bio.tool + id: bamtools
  • bio.tool ids: bamtools
  • biii: + nan
  • bio.tool name: BamTools
  • bio.tool description: + BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and + managing BAM files.
  • EDAM operation: Data handling, Sequence + alignment analysis
  • EDAM topic: Sequencing, Data management, + Sequence analysis
  • Status: Up-to-date
  • Source: + https://github.com/pezmaster31/bamtools
  • ToolShed categories: + Sequence Analysis, SAM
  • ToolShed id: bamtools
  • Date + of first commit of the suite: 2017-06-09
  • Galaxy wrapper + owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools
  • Galaxy + wrapper version: 2.5.2
  • Conda id: bamtools
  • Conda + version: 2.5.2
  • EDAM operation (no superclasses): + Data handling, Sequence alignment analysis
  • EDAM topic (no superclasses): + Sequencing, Sequence analysis
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 14693
  • No. of tool users (all time) (usegalaxy.eu): 15620
  • Tool + usage (5 years) (usegalaxy.eu): 653
  • Tool usage (all time) + (usegalaxy.eu): 721
  • No. of tool users (5 years) (usegalaxy.org): + 61872
  • No. of tool users (all time) (usegalaxy.org): 101400
  • Tool + usage (5 years) (usegalaxy.org): 1656
  • Tool usage (all time) + (usegalaxy.org): 5678
  • No. of tool users (5 years) (usegalaxy.org.au): + 39
  • No. of tool users (all time) (usegalaxy.org.au): 39
  • Tool + usage (5 years) (usegalaxy.org.au): 3
  • Tool usage (all time) + (usegalaxy.org.au): 3
  • No. of tool users (5 years) - all + main servers: 76604
  • No. of tool users (all time) - all + main servers: 117059
  • Tool usage (5 years) - all main servers: + 2312
  • Tool usage (all time) - all main servers: 6402
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: bamtools + - description_md: '
  • Galaxy tool ids: bandage_image, bandage_info
  • Description: + Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs + Easily
  • bio.tool id: bandage
  • bio.tool ids: + bandage
  • biii: nan
  • bio.tool name: Bandage
  • 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.
  • EDAM + operation: Sequence assembly visualisation
  • EDAM topic: + Genomics, Sequence assembly
  • Status: Up-to-date
  • Source: + https://github.com/rrwick/Bandage
  • ToolShed categories: + Visualization
  • ToolShed id: bandage
  • Date of + first commit of the suite: 2018-09-14
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage
  • Galaxy + wrapper version: 2022.09
  • Conda id: bandage_ng
  • Conda + version: 2022.09
  • EDAM operation (no superclasses): + Sequence assembly visualisation
  • EDAM topic (no superclasses): + Genomics, Sequence assembly
  • Available on UseGalaxy.org (Main): + 2
  • Available on UseGalaxy.org.au: 2
  • Available + on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 2
  • Tools + available on UseGalaxy.org (Main): 2
  • Tools available on + UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu: + 2
  • Tools available on UseGalaxy.fr: 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: 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.no: 2
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 55392
  • No. of tool users (all time) (usegalaxy.eu): 56095
  • Tool + usage (5 years) (usegalaxy.eu): 4951
  • Tool usage (all time) + (usegalaxy.eu): 5035
  • No. of tool users (5 years) (usegalaxy.org): + 47603
  • No. of tool users (all time) (usegalaxy.org): 47603
  • Tool + usage (5 years) (usegalaxy.org): 4916
  • Tool usage (all time) + (usegalaxy.org): 4916
  • No. of tool users (5 years) (usegalaxy.org.au): + 18089
  • No. of tool users (all time) (usegalaxy.org.au): + 18089
  • Tool usage (5 years) (usegalaxy.org.au): 3121
  • Tool + usage (all time) (usegalaxy.org.au): 3121
  • No. of tool users + (5 years) - all main servers: 121084
  • No. of tool users + (all time) - all main servers: 121787
  • Tool usage (5 years) + - all main servers: 12988
  • Tool usage (all time) - all main + servers: 13072
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: bandage + - description_md: '
  • Galaxy tool ids: BayeScan
  • Description: + Detecting natural selection from population-based genetic data
  • bio.tool + id: bayescan
  • bio.tool ids: bayescan
  • biii: + nan
  • bio.tool name: BayeScan
  • 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.
  • EDAM + operation: Statistical inference
  • EDAM topic: Genetics, + Evolutionary biology, Statistics and probability, DNA polymorphism
  • Status: + To update
  • Source: http://cmpg.unibe.ch/software/BayeScan/index.html
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: bayescan
  • Date + of first commit of the suite: 2017-03-09
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan
  • Galaxy + wrapper version: 2.1
  • Conda id: bayescan
  • Conda + version: 2.0.1
  • EDAM operation (no superclasses): + Statistical inference
  • EDAM topic (no superclasses): Genetics, + Evolutionary biology, Statistics and probability, DNA polymorphism
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 90
  • No. of tool + users (all time) (usegalaxy.eu): 90
  • Tool usage (5 years) + (usegalaxy.eu): 28
  • Tool usage (all time) (usegalaxy.eu): + 28
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 90
  • No. + of tool users (all time) - all main servers: 90
  • Tool usage + (5 years) - all main servers: 28
  • Tool usage (all time) + - all main servers: 28
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: bayescan + - description_md: '
  • Galaxy tool ids: bbtools_bbduk, bbtools_bbmap, + bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole
  • 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.
  • bio.tool id: bbmap
  • bio.tool + ids: bbmap, bbtools
  • biii: nan
  • bio.tool + name: BBMap
  • 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.
  • EDAM operation: 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
  • Status: + To update
  • Source: https://jgi.doe.gov/data-and-tools/bbtools/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: bbtools
  • Date + of first commit of the suite: 2021-10-04
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools
  • Galaxy + wrapper version: 39.08
  • Conda id: bbmap
  • Conda + version: 39.10
  • EDAM operation (no superclasses): + RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, + Read binning, Sequence alignment
  • EDAM topic (no superclasses): + RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq
  • Available + on UseGalaxy.org (Main): 6
  • Available on UseGalaxy.org.au: + 3
  • Available on UseGalaxy.eu: 5
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 6
  • Tools available on UseGalaxy.org.au: 3
  • Tools + available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 11989
  • No. of tool + users (all time) (usegalaxy.eu): 11989
  • Tool usage (5 years) + (usegalaxy.eu): 768
  • Tool usage (all time) (usegalaxy.eu): + 768
  • No. of tool users (5 years) (usegalaxy.org): 4458
  • No. + of tool users (all time) (usegalaxy.org): 4458
  • Tool usage + (5 years) (usegalaxy.org): 652
  • Tool usage (all time) (usegalaxy.org): + 652
  • No. of tool users (5 years) (usegalaxy.org.au): 2507
  • No. + of tool users (all time) (usegalaxy.org.au): 2507
  • Tool + usage (5 years) (usegalaxy.org.au): 80
  • Tool usage (all + time) (usegalaxy.org.au): 80
  • No. of tool users (5 years) + - all main servers: 18954
  • No. of tool users (all time) + - all main servers: 18954
  • Tool usage (5 years) - all main + servers: 1500
  • Tool usage (all time) - all main servers: + 1500
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: bbtools + - description_md: '
  • Galaxy tool ids: bigscape
  • Description: + Construct sequence similarity networks of BGCs and groups them into GCF
  • bio.tool + id: BiG-SCAPE
  • bio.tool ids: BiG-SCAPE
  • biii: + nan
  • bio.tool name: BiG-SCAPE
  • 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.
  • EDAM operation: Clustering, + Global alignment, Fold recognition
  • EDAM topic: Phylogeny, + Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families
  • Status: + Up-to-date
  • Source: https://github.com/medema-group/BiG-SCAPE
  • ToolShed + categories: Metagenomics
  • ToolShed id: bigscape
  • Date + of first commit of the suite: 2024-02-18
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape
  • Galaxy + wrapper version: 1.1.9
  • Conda id: bigscape
  • Conda + version: 1.1.9
  • EDAM operation (no superclasses): + Clustering, Global alignment, Fold recognition
  • EDAM topic (no + superclasses): Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, + Gene and protein families
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 544
  • No. of tool users (all time) (usegalaxy.eu): 544
  • Tool + usage (5 years) (usegalaxy.eu): 20
  • Tool usage (all time) + (usegalaxy.eu): 20
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 544
  • No. of tool users (all time) - all main + servers: 544
  • Tool usage (5 years) - all main servers: + 20
  • Tool usage (all time) - all main servers: 20
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: bigscape + - description_md: '
  • Galaxy tool ids: bin_refiner
  • Description: + Reconciles the outputs of different binning programs with the aim to improve + the quality of genome bins,especially with respect to contamination levels.
  • bio.tool + id: binning_refiner
  • bio.tool ids: binning_refiner
  • biii: + nan
  • bio.tool name: Binning_refiner
  • bio.tool + description: Improving genome bins through the combination of different + binning programs
  • EDAM operation: Read binning, Sequence + clustering
  • EDAM topic: Metagenomics, Sequence assembly, + Microbial ecology
  • Status: Up-to-date
  • Source: + https://github.com/songweizhi/Binning_refiner
  • ToolShed categories: + Metagenomics
  • ToolShed id: binning_refiner
  • Date + of first commit of the suite: 2022-02-18
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner
  • Galaxy + wrapper version: 1.4.3
  • Conda id: binning_refiner
  • Conda + version: 1.4.3
  • EDAM operation (no superclasses): + Read binning, Sequence clustering
  • EDAM topic (no superclasses): + Metagenomics, Sequence assembly, Microbial ecology
  • Available on + UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 126
  • No. of tool + users (all time) (usegalaxy.eu): 126
  • Tool usage (5 years) + (usegalaxy.eu): 42
  • Tool usage (all time) (usegalaxy.eu): + 42
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 126
  • No. + of tool users (all time) - all main servers: 126
  • Tool usage + (5 years) - all main servers: 42
  • Tool usage (all time) + - all main servers: 42
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: binning_refiner + - description_md: '
  • Galaxy tool ids: biohansel
  • Description: + Heidelberg and Enteritidis SNP Elucidation
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: https://github.com/phac-nml/biohansel
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: biohansel
  • Date + of first commit of the suite: 2018-08-01
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/biohansel
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel
  • Galaxy + wrapper version: 2.4.0
  • Conda id: bio_hansel
  • Conda + version: 2.6.1
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: biohansel + - description_md: '
  • Galaxy tool ids: biom_add_metadata, biom_convert, + biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table
  • Description: + The biom-format package provides a command line interface and Python API for + working with BIOM files.
  • bio.tool id: biomformat
  • bio.tool + ids: biomformat
  • biii: nan
  • bio.tool + name: biomformat
  • 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.
  • EDAM + operation: Formatting
  • EDAM topic: Laboratory information + management, Sequence analysis
  • Status: To update
  • Source: + https://github.com/biocore/biom-format
  • ToolShed categories: + Metagenomics
  • ToolShed id: nan
  • Date of first + commit of the suite: 2016-06-07
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format
  • Galaxy + wrapper version: 2.1.15
  • Conda id: biom-format
  • Conda + version: 2.1.7
  • EDAM operation (no superclasses): + Formatting
  • EDAM topic (no superclasses): Laboratory information + management, Sequence analysis
  • Available on UseGalaxy.org (Main): + 2
  • Available on UseGalaxy.org.au: 2
  • Available + on UseGalaxy.eu: 6
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 2
  • Tools available on + UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu: + 6
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 12725
  • No. of tool users (all time) (usegalaxy.eu): 12725
  • Tool + usage (5 years) (usegalaxy.eu): 297
  • Tool usage (all time) + (usegalaxy.eu): 297
  • No. of tool users (5 years) (usegalaxy.org): + 2851
  • No. of tool users (all time) (usegalaxy.org): 5049
  • Tool + usage (5 years) (usegalaxy.org): 450
  • Tool usage (all time) + (usegalaxy.org): 638
  • No. of tool users (5 years) (usegalaxy.org.au): + 2171
  • No. of tool users (all time) (usegalaxy.org.au): 2371
  • Tool + usage (5 years) (usegalaxy.org.au): 214
  • Tool usage (all + time) (usegalaxy.org.au): 239
  • No. of tool users (5 years) + - all main servers: 17747
  • No. of tool users (all time) + - all main servers: 20145
  • Tool usage (5 years) - all main + servers: 961
  • Tool usage (all time) - all main servers: + 1174
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: biom_format + - description_md: '
  • Galaxy tool ids: bacteria_tradis, tradis_essentiality, + tradis_gene_insert_sites
  • Description: Bio-Tradis is a tool + suite dedicated to essentiality analyses with TraDis data.
  • bio.tool + id: biotradis
  • bio.tool ids: biotradis
  • biii: + nan
  • bio.tool name: biotradis
  • 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.
  • EDAM operation: Sequence analysis
  • EDAM + topic: Mobile genetic elements, Workflows
  • Status: + Up-to-date
  • Source: https://www.sanger.ac.uk/science/tools/bio-tradis
  • ToolShed + categories: Genome annotation
  • ToolShed id: biotradis
  • Date + of first commit of the suite: 2020-01-17
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis
  • Galaxy + wrapper version: 1.4.5
  • Conda id: biotradis
  • Conda + version: 1.4.5
  • EDAM operation (no superclasses): + Sequence analysis
  • EDAM topic (no superclasses): Mobile + genetic elements, Workflows
  • Available on UseGalaxy.org (Main): + 3
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 3
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 6243
  • No. of tool users (all time) (usegalaxy.org): 6243
  • Tool + usage (5 years) (usegalaxy.org): 375
  • Tool usage (all time) + (usegalaxy.org): 375
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 6243
  • No. of tool users (all time) - all main + servers: 6243
  • Tool usage (5 years) - all main servers: + 375
  • Tool usage (all time) - all main servers: 375
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: biotradis + - description_md: '
  • Galaxy tool ids: blast2go
  • Description: + Maps BLAST results to GO annotation terms
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
  • ToolShed + categories: Ontology Manipulation, Sequence Analysis
  • ToolShed + id: blast2go
  • Date of first commit of the suite: + 2015-12-08
  • Galaxy wrapper owner: peterjc
  • Galaxy + wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
  • Galaxy + wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
  • Galaxy + wrapper version: 0.0.11
  • Conda id: b2g4pipe
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1063
  • No. of tool users (all time) (usegalaxy.eu): 1237
  • Tool + usage (5 years) (usegalaxy.eu): 257
  • Tool usage (all time) + (usegalaxy.eu): 300
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 1063
  • No. of tool users (all time) - all main + servers: 1237
  • Tool usage (5 years) - all main servers: + 257
  • Tool usage (all time) - all main servers: 300
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: blast2go + - description_md: '
  • Galaxy tool ids: blast_reciprocal_best_hits
  • Description: + BLAST Reciprocal Best Hits (RBH) from two FASTA files
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
  • ToolShed + categories: Fasta Manipulation, Sequence Analysis
  • ToolShed + id: blast_rbh
  • Date of first commit of the suite: + 2016-12-05
  • Galaxy wrapper owner: peterjc
  • Galaxy + wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
  • Galaxy + wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
  • Galaxy + wrapper version: 0.3.0
  • Conda id: biopython
  • Conda + version: 1.70
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 24916
  • No. of tool + users (all time) (usegalaxy.eu): 27120
  • Tool usage (5 years) + (usegalaxy.eu): 283
  • Tool usage (all time) (usegalaxy.eu): + 347
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 24916
  • No. + of tool users (all time) - all main servers: 27120
  • Tool + usage (5 years) - all main servers: 283
  • Tool usage (all + time) - all main servers: 347
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: blast_rbh + - description_md: '
  • Galaxy tool ids: blastxml_to_top_descr
  • Description: + Make table of top BLAST match descriptions
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
  • ToolShed + categories: Convert Formats, Sequence Analysis, Text Manipulation
  • ToolShed + id: blastxml_to_top_descr
  • Date of first commit of the suite: + 2015-05-21
  • Galaxy wrapper owner: peterjc
  • Galaxy + wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
  • Galaxy + wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
  • Galaxy + wrapper version: 0.1.2
  • Conda id: python
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 264392
  • No. of tool users (all time) (usegalaxy.eu): 265217
  • Tool + usage (5 years) (usegalaxy.eu): 483
  • Tool usage (all time) + (usegalaxy.eu): 552
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 264392
  • No. of tool users (all time) - all + main servers: 265217
  • Tool usage (5 years) - all main servers: + 483
  • Tool usage (all time) - all main servers: 552
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: blastxml_to_top_descr + - description_md: '
  • Galaxy tool ids: est_abundance
  • Description: + Bayesian Reestimation of Abundance with KrakEN
  • bio.tool id: + bracken
  • bio.tool ids: bracken
  • biii: + nan
  • bio.tool name: Bracken
  • bio.tool description: + Statistical method that computes the abundance of species in DNA sequences from + a metagenomics sample.
  • EDAM operation: Statistical calculation
  • EDAM + topic: Metagenomics, Microbial ecology
  • Status: Up-to-date
  • Source: + https://ccb.jhu.edu/software/bracken/
  • ToolShed categories: + Sequence Analysis, Metagenomics
  • ToolShed id: bracken
  • Date + of first commit of the suite: 2019-10-15
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken
  • Galaxy + wrapper version: 3.0
  • Conda id: bracken
  • Conda + version: 3.0
  • EDAM operation (no superclasses): Statistical + calculation
  • EDAM topic (no superclasses): Metagenomics, + Microbial ecology
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 51378
  • No. of tool + users (all time) (usegalaxy.eu): 51378
  • Tool usage (5 years) + (usegalaxy.eu): 775
  • Tool usage (all time) (usegalaxy.eu): + 775
  • No. of tool users (5 years) (usegalaxy.org): 3298
  • No. + of tool users (all time) (usegalaxy.org): 3298
  • Tool usage + (5 years) (usegalaxy.org): 160
  • Tool usage (all time) (usegalaxy.org): + 160
  • No. of tool users (5 years) (usegalaxy.org.au): 1660
  • No. + of tool users (all time) (usegalaxy.org.au): 1660
  • Tool + usage (5 years) (usegalaxy.org.au): 63
  • Tool usage (all + time) (usegalaxy.org.au): 63
  • No. of tool users (5 years) + - all main servers: 56336
  • No. of tool users (all time) + - all main servers: 56336
  • Tool usage (5 years) - all main + servers: 998
  • Tool usage (all time) - all main servers: + 998
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: bracken + - description_md: '
  • Galaxy tool ids: busco
  • Description: + BUSCO assess genome and annotation completeness
  • bio.tool id: + busco
  • bio.tool ids: busco
  • biii: nan
  • bio.tool + name: BUSCO
  • 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.
  • EDAM operation: Sequence + assembly validation, Scaffolding, Genome assembly, Transcriptome assembly
  • EDAM + topic: Sequence assembly, Genomics, Transcriptomics, Sequence analysis
  • Status: + To update
  • Source: https://gitlab.com/ezlab/busco/-/releases
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: busco
  • Date + of first commit of the suite: 2019-12-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco
  • Galaxy + wrapper version: 5.7.1
  • Conda id: busco
  • Conda + version: 5.8.0
  • EDAM operation (no superclasses): + Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly
  • EDAM + topic (no superclasses): Sequence assembly, Transcriptomics, Sequence + analysis
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 102717
  • No. of tool + users (all time) (usegalaxy.eu): 103051
  • Tool usage (5 years) + (usegalaxy.eu): 3877
  • Tool usage (all time) (usegalaxy.eu): + 3926
  • No. of tool users (5 years) (usegalaxy.org): 34251
  • No. + of tool users (all time) (usegalaxy.org): 34251
  • Tool usage + (5 years) (usegalaxy.org): 3506
  • Tool usage (all time) (usegalaxy.org): + 3506
  • No. of tool users (5 years) (usegalaxy.org.au): 33192
  • No. + of tool users (all time) (usegalaxy.org.au): 34369
  • Tool + usage (5 years) (usegalaxy.org.au): 2439
  • Tool usage (all + time) (usegalaxy.org.au): 2525
  • No. of tool users (5 years) + - all main servers: 170160
  • No. of tool users (all time) + - all main servers: 171671
  • Tool usage (5 years) - all main + servers: 9822
  • Tool usage (all time) - all main servers: + 9957
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: busco + - description_md: '
  • Galaxy tool ids: cat_add_names, cat_bins, + cat_contigs, cat_prepare, cat_summarise
  • Description: Contig + Annotation Tool (CAT)
  • bio.tool id: cat_bins
  • bio.tool + ids: cat_bins
  • biii: nan
  • bio.tool name: + CAT and BAT
  • 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.
  • EDAM + operation: Taxonomic classification, Sequence assembly, Coding region + prediction
  • EDAM topic: Metagenomics, Metagenomic sequencing, + Taxonomy, Sequence assembly
  • Status: To update
  • Source: + https://github.com/dutilh/CAT
  • ToolShed categories: Metagenomics
  • ToolShed + id: contig_annotation_tool
  • Date of first commit of the + suite: 2019-11-27
  • Galaxy wrapper owner: iuc
  • Galaxy + wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat
  • Galaxy + wrapper version: 5.2.3
  • Conda id: cat
  • Conda + version: 5.3
  • EDAM operation (no superclasses): Taxonomic + classification, Sequence assembly, Coding region prediction
  • EDAM + topic (no superclasses): Metagenomics, Metagenomic sequencing, Taxonomy, + Sequence assembly
  • Available on UseGalaxy.org (Main): 5
  • Available + on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: + 5
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 5
  • Tools available on UseGalaxy.org.au: + 2
  • Tools available on UseGalaxy.eu: 5
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 5
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 3835
  • No. of tool + users (all time) (usegalaxy.eu): 3835
  • Tool usage (5 years) + (usegalaxy.eu): 597
  • Tool usage (all time) (usegalaxy.eu): + 597
  • No. of tool users (5 years) (usegalaxy.org): 1359
  • No. + of tool users (all time) (usegalaxy.org): 1359
  • Tool usage + (5 years) (usegalaxy.org): 467
  • Tool usage (all time) (usegalaxy.org): + 467
  • No. of tool users (5 years) (usegalaxy.org.au): 646
  • No. + of tool users (all time) (usegalaxy.org.au): 646
  • Tool usage + (5 years) (usegalaxy.org.au): 98
  • Tool usage (all time) + (usegalaxy.org.au): 98
  • No. of tool users (5 years) - all + main servers: 5840
  • No. of tool users (all time) - all main + servers: 5840
  • Tool usage (5 years) - all main servers: + 1162
  • Tool usage (all time) - all main servers: 1162
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: cat + - description_md: '
  • Galaxy tool ids: cd_hit_dup
  • Description: + simple tool for removing duplicates from sequencing reads
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: nan
  • ToolShed + categories: Metagenomics, Sequence Analysis
  • ToolShed id: + cd_hit_dup
  • Date of first commit of the suite: 2015-04-28
  • Galaxy + wrapper owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup
  • Galaxy + wrapper version: 0.0.1
  • Conda id: cd-hit-auxtools
  • Conda + version: 4.8.1
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 5946
  • No. of tool + users (all time) (usegalaxy.org): 7379
  • Tool usage (5 years) + (usegalaxy.org): 407
  • Tool usage (all time) (usegalaxy.org): + 628
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 5946
  • No. + of tool users (all time) - all main servers: 7379
  • Tool + usage (5 years) - all main servers: 407
  • Tool usage (all + time) - all main servers: 628
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: cd_hit_dup + - description_md: '
  • Galaxy tool ids: cd_hit
  • Description: + Cluster or compare biological sequence datasets
  • bio.tool id: + cd-hit
  • bio.tool ids: cd-hit
  • biii: + nan
  • bio.tool name: cd-hit
  • bio.tool description: + Cluster a nucleotide dataset into representative sequences.
  • EDAM + operation: Sequence clustering
  • EDAM topic: Sequencing
  • Status: + Up-to-date
  • Source: http://weizhongli-lab.org/cd-hit/
  • ToolShed + categories: Sequence Analysis, Fasta Manipulation
  • ToolShed + id: cd_hit
  • Date of first commit of the suite: 2018-02-26
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit
  • Galaxy + wrapper version: 4.8.1
  • Conda id: cd-hit
  • Conda + version: 4.8.1
  • EDAM operation (no superclasses): + Sequence clustering
  • EDAM topic (no superclasses): Sequencing
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 10414
  • No. of tool + users (all time) (usegalaxy.eu): 10414
  • Tool usage (5 years) + (usegalaxy.eu): 510
  • Tool usage (all time) (usegalaxy.eu): + 510
  • No. of tool users (5 years) (usegalaxy.org): 2
  • No. + of tool users (all time) (usegalaxy.org): 2
  • Tool usage + (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): + 1
  • No. of tool users (5 years) (usegalaxy.org.au): 2
  • No. + of tool users (all time) (usegalaxy.org.au): 2
  • Tool usage + (5 years) (usegalaxy.org.au): 1
  • Tool usage (all time) (usegalaxy.org.au): + 1
  • No. of tool users (5 years) - all main servers: 10418
  • No. + of tool users (all time) - all main servers: 10418
  • Tool + usage (5 years) - all main servers: 512
  • Tool usage (all + time) - all main servers: 512
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: cdhit + - description_md: '
  • Galaxy tool ids: cemitool
  • Description: + Gene co-expression network analysis tool
  • bio.tool id: cemitool
  • bio.tool + ids: cemitool
  • biii: nan
  • bio.tool name: + CEMiTool
  • 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.
  • EDAM operation: Enrichment analysis, + Pathway or network analysis
  • EDAM topic: Gene expression, + Transcriptomics, Microarray experiment
  • Status: Up-to-date
  • Source: + https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html
  • ToolShed + categories: Transcriptomics, RNA, Statistics
  • ToolShed id: + cemitool
  • Date of first commit of the suite: 2022-10-10
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool
  • Galaxy + wrapper version: 1.26.0
  • Conda id: bioconductor-cemitool
  • Conda + version: 1.26.0
  • EDAM operation (no superclasses): + Enrichment analysis, Pathway or network analysis
  • EDAM topic (no + superclasses): Transcriptomics, Microarray experiment
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 225
  • No. of tool + users (all time) (usegalaxy.eu): 225
  • Tool usage (5 years) + (usegalaxy.eu): 32
  • Tool usage (all time) (usegalaxy.eu): + 32
  • No. of tool users (5 years) (usegalaxy.org): 271
  • No. + of tool users (all time) (usegalaxy.org): 271
  • Tool usage + (5 years) (usegalaxy.org): 61
  • Tool usage (all time) (usegalaxy.org): + 61
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 496
  • No. + of tool users (all time) - all main servers: 496
  • Tool usage + (5 years) - all main servers: 93
  • Tool usage (all time) + - all main servers: 93
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: cemitool + - description_md: '
  • 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
  • Description: + Assess the quality of microbial genomes recovered from isolates, single cells, + and metagenomes
  • bio.tool id: checkm
  • bio.tool + ids: checkm
  • biii: nan
  • bio.tool name: + CheckM
  • bio.tool description: CheckM provides a set of tools + for assessing the quality of genomes recovered from isolates, single cells, + or metagenomes.
  • EDAM operation: Sequence assembly validation, + Validation, Sequence composition calculation, Sequencing quality control, Statistical + calculation
  • EDAM topic: Genomics, Phylogenomics, Phylogenetics, + Taxonomy, Metagenomics, Data quality management
  • Status: + Up-to-date
  • Source: https://github.com/Ecogenomics/CheckM
  • ToolShed + categories: Metagenomics
  • ToolShed id: checkm
  • Date + of first commit of the suite: 2022-07-29
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm
  • Galaxy + wrapper version: 1.2.3
  • Conda id: checkm-genome
  • Conda + version: 1.2.3
  • EDAM operation (no superclasses): + Sequence assembly validation, Sequence composition calculation, Statistical + calculation
  • EDAM topic (no superclasses): Phylogenomics, + Phylogenetics, Taxonomy, Metagenomics, Data quality management
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 10
  • Available on UseGalaxy.eu: 10
  • Available + on UseGalaxy.fr: 10
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 10
  • Tools + available on UseGalaxy.eu: 10
  • Tools available on UseGalaxy.fr: + 10
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 7500
  • No. of tool + users (all time) (usegalaxy.eu): 7500
  • Tool usage (5 years) + (usegalaxy.eu): 930
  • Tool usage (all time) (usegalaxy.eu): + 930
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 7500
  • No. + of tool users (all time) - all main servers: 7500
  • Tool + usage (5 years) - all main servers: 930
  • Tool usage (all + time) - all main servers: 930
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: checkm + - description_md: '
  • Galaxy tool ids: clair3
  • Description: + Symphonizing pileup and full-alignment for high-performance long-read variant + calling
  • bio.tool id: clair3
  • bio.tool ids: + clair3
  • biii: nan
  • bio.tool name: Clair3
  • 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.
  • EDAM operation: Variant calling
  • EDAM + topic: Molecular genetics
  • Status: To update
  • Source: + https://github.com/HKU-BAL/Clair3
  • ToolShed categories: + Sequence Analysis, Variant Analysis
  • ToolShed id: clair3
  • Date + of first commit of the suite: 2022-06-15
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3
  • Galaxy + wrapper version: 1.0.8
  • Conda id: clair3
  • Conda + version: 1.0.10
  • EDAM operation (no superclasses): + Variant calling
  • EDAM topic (no superclasses): Molecular + genetics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 3388
  • No. of tool + users (all time) (usegalaxy.eu): 3388
  • Tool usage (5 years) + (usegalaxy.eu): 187
  • Tool usage (all time) (usegalaxy.eu): + 187
  • No. of tool users (5 years) (usegalaxy.org): 1
  • No. + of tool users (all time) (usegalaxy.org): 1
  • Tool usage + (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): + 1
  • No. of tool users (5 years) (usegalaxy.org.au): 1
  • No. + of tool users (all time) (usegalaxy.org.au): 1
  • Tool usage + (5 years) (usegalaxy.org.au): 1
  • Tool usage (all time) (usegalaxy.org.au): + 1
  • No. of tool users (5 years) - all main servers: 3390
  • No. + of tool users (all time) - all main servers: 3390
  • Tool + usage (5 years) - all main servers: 189
  • Tool usage (all + time) - all main servers: 189
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: clair3 + - description_md: '
  • Galaxy tool ids: clinod
  • Description: + NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins
  • bio.tool + id: clinod
  • bio.tool ids: clinod
  • biii: + nan
  • bio.tool name: clinod
  • 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.
  • EDAM + operation: Nucleic acid sequence analysis
  • EDAM topic: + Sequence analysis
  • Status: To update
  • Source: + http://www.compbio.dundee.ac.uk/www-nod/
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: clinod
  • Date + of first commit of the suite: 2014-02-18
  • Galaxy wrapper + owner: peterjc
  • Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
  • Galaxy + wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
  • Galaxy + wrapper version: 0.1.0
  • Conda id: clinod
  • Conda + version: 1.3
  • EDAM operation (no superclasses): Nucleic + acid sequence analysis
  • EDAM topic (no superclasses): Sequence + analysis
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 0
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 0
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 548
  • No. of tool + users (all time) (usegalaxy.org): 548
  • Tool usage (5 years) + (usegalaxy.org): 18
  • Tool usage (all time) (usegalaxy.org): + 18
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 548
  • No. + of tool users (all time) - all main servers: 548
  • Tool usage + (5 years) - all main servers: 18
  • Tool usage (all time) + - all main servers: 18
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: clinod + - description_md: '
  • Galaxy tool ids: clustalw
  • Description: + ClustalW multiple sequence alignment program for DNA or proteins
  • bio.tool + id: clustal2
  • bio.tool ids: clustal2
  • biii: + nan
  • bio.tool name: Clustal 2 (Clustal W, Clustal X)
  • 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.
  • EDAM operation: Multiple + sequence alignment
  • EDAM topic: Phylogeny, Sequence analysis
  • Status: + Up-to-date
  • Source: http://www.clustal.org/clustal2/
  • ToolShed + categories: Phylogenetics, Sequence Analysis
  • ToolShed id: + clustalw
  • Date of first commit of the suite: 2022-10-02
  • Galaxy + wrapper owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw
  • Galaxy + wrapper version: 2.1
  • Conda id: clustalw
  • Conda + version: 2.1
  • EDAM operation (no superclasses): Multiple + sequence alignment
  • EDAM topic (no superclasses): Phylogeny, + Sequence analysis
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 79867
  • No. of tool + users (all time) (usegalaxy.eu): 80817
  • Tool usage (5 years) + (usegalaxy.eu): 1675
  • Tool usage (all time) (usegalaxy.eu): + 1785
  • No. of tool users (5 years) (usegalaxy.org): 49493
  • No. + of tool users (all time) (usegalaxy.org): 87884
  • Tool usage + (5 years) (usegalaxy.org): 3703
  • Tool usage (all time) (usegalaxy.org): + 7380
  • No. of tool users (5 years) (usegalaxy.org.au): 8797
  • No. + of tool users (all time) (usegalaxy.org.au): 9713
  • Tool + usage (5 years) (usegalaxy.org.au): 670
  • Tool usage (all + time) (usegalaxy.org.au): 728
  • No. of tool users (5 years) + - all main servers: 138157
  • No. of tool users (all time) + - all main servers: 178414
  • Tool usage (5 years) - all main + servers: 6048
  • Tool usage (all time) - all main servers: + 9893
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: clustalw + - description_md: '
  • Galaxy tool ids: cmsearch_deoverlap
  • Description: + removes lower scoring overlaps from cmsearch results.
  • bio.tool + id: cmsearch-deoverlap
  • bio.tool ids: cmsearch-deoverlap
  • biii: + nan
  • bio.tool name: cmsearch-deoverlap
  • bio.tool + description: Removes lower scoring overlaps from cmsearch results.
  • EDAM + operation: Comparison, Alignment
  • EDAM topic: Biology, + Medicine
  • Status: To update
  • Source: + https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl
  • ToolShed + categories: RNA
  • ToolShed id: cmsearch_deoverlap
  • Date + of first commit of the suite: 2023-08-19
  • Galaxy wrapper + owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap
  • Galaxy + wrapper version: 0.08+galaxy2
  • Conda id: perl
  • Conda + version: nan
  • EDAM operation (no superclasses): Comparison, + Alignment
  • EDAM topic (no superclasses): Biology, Medicine
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 2609
  • No. of tool + users (all time) (usegalaxy.eu): 2609
  • Tool usage (5 years) + (usegalaxy.eu): 3
  • Tool usage (all time) (usegalaxy.eu): + 3
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 2609
  • No. + of tool users (all time) - all main servers: 2609
  • Tool + usage (5 years) - all main servers: 3
  • Tool usage (all time) + - all main servers: 3
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: cmsearch_deoverlap + - description_md: '
  • Galaxy tool ids: codeml
  • Description: + Detects positive selection
  • bio.tool id: paml
  • bio.tool + ids: paml
  • biii: nan
  • bio.tool name: + PAML
  • bio.tool description: Package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.
  • EDAM + operation: Probabilistic sequence generation, Phylogenetic tree generation + (maximum likelihood and Bayesian methods), Phylogenetic tree analysis
  • EDAM + topic: Phylogenetics, Sequence analysis
  • Status: + To update
  • Source: http://abacus.gene.ucl.ac.uk/software/paml.html
  • ToolShed + categories: Phylogenetics
  • ToolShed id: codeml
  • Date + of first commit of the suite: 2017-07-19
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml
  • Galaxy + wrapper version: 4.9
  • Conda id: paml
  • Conda + version: 4.10.7
  • EDAM operation (no superclasses): + Probabilistic sequence generation
  • EDAM topic (no superclasses): + Phylogenetics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 61197
  • No. of tool + users (all time) (usegalaxy.eu): 61220
  • Tool usage (5 years) + (usegalaxy.eu): 64
  • Tool usage (all time) (usegalaxy.eu): + 65
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 61197
  • No. + of tool users (all time) - all main servers: 61220
  • Tool + usage (5 years) - all main servers: 64
  • Tool usage (all + time) - all main servers: 65
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: codeml + - description_md: '
  • Galaxy tool ids: cooc_mutbamscan, cooc_pubmut, + cooc_tabmut
  • Description: co-occurrence of mutations on + amplicons
  • bio.tool id: cojac
  • bio.tool ids: + cojac
  • biii: nan
  • bio.tool name: COJAC
  • 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.
  • EDAM operation: + nan
  • EDAM topic: Genetic variation
  • Status: + Up-to-date
  • Source: https://github.com/cbg-ethz/cojac
  • ToolShed + categories: Metagenomics, Sequence Analysis
  • ToolShed id: + cojac
  • Date of first commit of the suite: 2022-08-11
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac
  • Galaxy + wrapper version: 0.9.2
  • Conda id: cojac
  • Conda + version: 0.9.2
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): Genetic variation
  • Available + on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 3
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 2
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 2758
  • No. of tool + users (all time) (usegalaxy.eu): 2758
  • Tool usage (5 years) + (usegalaxy.eu): 22
  • Tool usage (all time) (usegalaxy.eu): + 22
  • No. of tool users (5 years) (usegalaxy.org): 20
  • No. + of tool users (all time) (usegalaxy.org): 20
  • Tool usage + (5 years) (usegalaxy.org): 10
  • Tool usage (all time) (usegalaxy.org): + 10
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 2778
  • No. + of tool users (all time) - all main servers: 2778
  • Tool + usage (5 years) - all main servers: 32
  • Tool usage (all + time) - all main servers: 32
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: cojac + - description_md: '
  • Galaxy tool ids: combine_stats
  • Description: + Combine multiple Assemblystats datasets into a single tabular report
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/phac-nml/galaxy_tools
  • ToolShed + categories: Assembly
  • ToolShed id: combine_assemblystats
  • Date + of first commit of the suite: 2017-11-08
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats
  • Galaxy + wrapper version: 1.0
  • Conda id: perl-getopt-long
  • Conda + version: 2.58
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: combine_assembly_stats + - description_md: '
  • Galaxy tool ids: combine_metaphlan_humann
  • Description: + Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and + gene families/pathways abundances
  • bio.tool id: combine_metaphlan_and_humann
  • bio.tool + ids: combine_metaphlan_and_humann
  • biii: nan
  • bio.tool + name: Combine Metaphlan and HUMAnN
  • bio.tool description: + This tool combine MetaPhlAn outputs and HUMANnN outputs
  • EDAM operation: + Aggregation
  • EDAM topic: Metagenomics, Molecular interactions, + pathways and networks
  • Status: To update
  • Source: + nan
  • ToolShed categories: Metagenomics
  • ToolShed + id: combine_metaphlan2_humann2
  • Date of first commit of + the suite: 2023-07-20
  • Galaxy wrapper owner: bebatut
  • Galaxy + wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann
  • Galaxy + wrapper version: 0.3.0
  • Conda id: python
  • Conda + version: nan
  • EDAM operation (no superclasses): Aggregation
  • EDAM + topic (no superclasses): Metagenomics, Molecular interactions, pathways + and networks
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 530
  • No. of tool + users (all time) (usegalaxy.eu): 530
  • Tool usage (5 years) + (usegalaxy.eu): 65
  • Tool usage (all time) (usegalaxy.eu): + 65
  • No. of tool users (5 years) (usegalaxy.org): 8
  • No. + of tool users (all time) (usegalaxy.org): 8
  • Tool usage + (5 years) (usegalaxy.org): 6
  • Tool usage (all time) (usegalaxy.org): + 6
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 538
  • No. + of tool users (all time) - all main servers: 538
  • Tool usage + (5 years) - all main servers: 71
  • Tool usage (all time) + - all main servers: 71
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: combine_metaphlan_humann + - description_md: '
  • Galaxy tool ids: compare_humann2_output
  • Description: + Compare outputs of HUMAnN2 for several samples and extract similar and specific + information
  • bio.tool id: compare_humann2_outputs
  • bio.tool + ids: compare_humann2_outputs
  • biii: nan
  • bio.tool + name: Compare HUMAnN2 outputs
  • bio.tool description: + This tool compare HUMANnN2 outputs with gene families or pathways and their + relative abundances between several samples
  • EDAM operation: + Comparison
  • EDAM topic: Metagenomics, Gene and protein families
  • Status: + To update
  • Source: nan
  • ToolShed categories: + Metagenomics
  • ToolShed id: compare_humann2_output
  • Date + of first commit of the suite: 2022-10-19
  • Galaxy wrapper + owner: bebatut
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
  • Galaxy + wrapper version: 0.2.0
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): Comparison
  • EDAM + topic (no superclasses): Metagenomics, Gene and protein families
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 306
  • No. of tool + users (all time) (usegalaxy.eu): 332
  • Tool usage (5 years) + (usegalaxy.eu): 28
  • Tool usage (all time) (usegalaxy.eu): + 32
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 306
  • No. + of tool users (all time) - all main servers: 332
  • Tool usage + (5 years) - all main servers: 28
  • Tool usage (all time) + - all main servers: 32
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: compare_humann2_output + - description_md: '
  • Galaxy tool ids: compleasm
  • Description: + Compleasm: a faster and more accurate reimplementation of BUSCO
  • bio.tool + id: compleasm
  • bio.tool ids: compleasm
  • biii: + nan
  • bio.tool name: compleasm
  • bio.tool description: + "Compleasm: a faster and more accurate reimplementation of BUSCO"
  • EDAM + operation: Sequence assembly validation, Sequence analysis, Scaffolding, + Transcriptome assembly
  • EDAM topic: Sequence assembly, Genomics, + Transcriptomics, Sequence analysis
  • Status: Up-to-date
  • Source: + https://github.com/huangnengCSU/compleasm
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: compleasm
  • Date + of first commit of the suite: 2023-12-04
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm
  • Galaxy + wrapper version: 0.2.6
  • Conda id: compleasm
  • Conda + version: 0.2.6
  • EDAM operation (no superclasses): + Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome + assembly
  • EDAM topic (no superclasses): Sequence assembly, + Transcriptomics, Sequence analysis
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 266
  • No. of tool users (all time) (usegalaxy.eu): 266
  • Tool + usage (5 years) (usegalaxy.eu): 39
  • Tool usage (all time) + (usegalaxy.eu): 39
  • No. of tool users (5 years) (usegalaxy.org): + 28
  • No. of tool users (all time) (usegalaxy.org): 28
  • Tool + usage (5 years) (usegalaxy.org): 15
  • Tool usage (all time) + (usegalaxy.org): 15
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 294
  • No. of tool users (all time) - all main + servers: 294
  • Tool usage (5 years) - all main servers: + 54
  • Tool usage (all time) - all main servers: 54
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: compleasm + - description_md: '
  • Galaxy tool ids: concoct, concoct_coverage_table, + concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering
  • 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.
  • bio.tool id: concoct
  • bio.tool + ids: concoct
  • biii: nan
  • bio.tool name: + CONCOCT
  • 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.
  • EDAM + operation: Sequence clustering, Read binning
  • EDAM topic: + Metagenomics
  • Status: Up-to-date
  • Source: + https://github.com/BinPro/CONCOCT
  • ToolShed categories: + Metagenomics
  • ToolShed id: concoct
  • Date of + first commit of the suite: 2022-02-18
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct
  • Galaxy + wrapper version: 1.1.0
  • Conda id: concoct
  • Conda + version: 1.1.0
  • EDAM operation (no superclasses): + Sequence clustering, Read binning
  • EDAM topic (no superclasses): + Metagenomics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 5
  • Available on UseGalaxy.fr: 5
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 5
  • Tools + available on UseGalaxy.fr: 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 2105
  • No. of tool + users (all time) (usegalaxy.eu): 2105
  • Tool usage (5 years) + (usegalaxy.eu): 155
  • Tool usage (all time) (usegalaxy.eu): + 155
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 2105
  • No. + of tool users (all time) - all main servers: 2105
  • Tool + usage (5 years) - all main servers: 155
  • Tool usage (all + time) - all main servers: 155
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: concoct + - description_md: '
  • Galaxy tool ids: coverm_contig, coverm_genome
  • Description: + CoverM genome and contig wrappers
  • bio.tool id: coverm
  • bio.tool + ids: coverm
  • biii: nan
  • bio.tool name: + CoverM
  • bio.tool description: Read coverage calculator for + metagenomics
  • EDAM operation: Local alignment
  • EDAM + topic: Bioinformatics
  • Status: Up-to-date
  • Source: + https://github.com/wwood/CoverM
  • ToolShed categories: Sequence + Analysis
  • ToolShed id: coverm
  • Date of first + commit of the suite: 2022-04-26
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tools/coverm
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm
  • Galaxy + wrapper version: 0.7.0
  • Conda id: coverm
  • Conda + version: 0.7.0
  • EDAM operation (no superclasses): + Local alignment
  • EDAM topic (no superclasses): Bioinformatics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: + 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1081
  • No. of tool + users (all time) (usegalaxy.eu): 1081
  • Tool usage (5 years) + (usegalaxy.eu): 151
  • Tool usage (all time) (usegalaxy.eu): + 151
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1081
  • No. + of tool users (all time) - all main servers: 1081
  • Tool + usage (5 years) - all main servers: 151
  • Tool usage (all + time) - all main servers: 151
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: coverm + - description_md: '
  • Galaxy tool ids: CryptoGenotyper
  • Description: + CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype + based on SSU rRNA and gp60 markers.
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: + https://github.com/phac-nml/CryptoGenotyper
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: cryptogenotyper
  • Date + of first commit of the suite: 2020-10-14
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/CryptoGenotyper
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper
  • Galaxy + wrapper version: 1.0
  • Conda id: cryptogenotyper
  • Conda + version: 1.0
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 9942
  • No. of tool users (all time) (usegalaxy.eu): 9942
  • Tool + usage (5 years) (usegalaxy.eu): 26
  • Tool usage (all time) + (usegalaxy.eu): 26
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 9942
  • No. of tool users (all time) - all main + servers: 9942
  • Tool usage (5 years) - all main servers: + 26
  • Tool usage (all time) - all main servers: 26
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: cryptogenotyper + - description_md: '
  • Galaxy tool ids: cutadapt
  • Description: + Flexible tool to remove adapter sequences (and quality trim) high throughput + sequencing reads (fasta/fastq).
  • bio.tool id: cutadapt
  • bio.tool + ids: cutadapt
  • biii: nan
  • bio.tool name: + Cutadapt
  • bio.tool description: Find and remove adapter + sequences, primers, poly-A tails and other types of unwanted sequence from your + high-throughput sequencing reads.
  • EDAM operation: Sequence + trimming, Primer removal, Read pre-processing
  • EDAM topic: + Genomics, Probes and primers, Sequencing
  • Status: Up-to-date
  • Source: + https://cutadapt.readthedocs.org/en/stable/
  • ToolShed categories: + Fasta Manipulation, Fastq Manipulation, Sequence Analysis
  • ToolShed + id: cutadapt
  • Date of first commit of the suite: + 2023-11-03
  • Galaxy wrapper owner: lparsons
  • Galaxy + wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt
  • Galaxy + wrapper version: 4.9
  • Conda id: cutadapt
  • Conda + version: 4.9
  • EDAM operation (no superclasses): Sequence + trimming, Primer removal, Read pre-processing
  • EDAM topic (no superclasses): + Genomics, Probes and primers, Sequencing
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 259754
  • No. of tool users (all time) (usegalaxy.eu): 272370
  • Tool + usage (5 years) (usegalaxy.eu): 11716
  • Tool usage (all time) + (usegalaxy.eu): 12601
  • No. of tool users (5 years) (usegalaxy.org): + 334550
  • No. of tool users (all time) (usegalaxy.org): 362356
  • Tool + usage (5 years) (usegalaxy.org): 18618
  • Tool usage (all + time) (usegalaxy.org): 20162
  • No. of tool users (5 years) + (usegalaxy.org.au): 64377
  • No. of tool users (all time) + (usegalaxy.org.au): 65986
  • Tool usage (5 years) (usegalaxy.org.au): + 3507
  • Tool usage (all time) (usegalaxy.org.au): 3627
  • No. + of tool users (5 years) - all main servers: 658681
  • No. + of tool users (all time) - all main servers: 700712
  • Tool + usage (5 years) - all main servers: 33841
  • Tool usage (all + time) - all main servers: 36390
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: cutadapt + - description_md: '
  • Galaxy tool ids: dada2_assignTaxonomyAddspecies, + dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, + dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, + dada2_seqCounts
  • Description: DADA2 wrappers
  • bio.tool + id: dada2
  • bio.tool ids: dada2
  • biii: + nan
  • bio.tool name: dada2
  • 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.
  • EDAM + operation: Variant calling, DNA barcoding
  • EDAM topic: + Sequencing, Genetic variation, Microbial ecology, Metagenomics
  • Status: + To update
  • Source: https://benjjneb.github.io/dada2/index.html
  • ToolShed + categories: Metagenomics
  • ToolShed id: dada2
  • Date + of first commit of the suite: 2019-07-05
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2
  • Galaxy + wrapper version: nan
  • Conda id: bioconductor-dada2
  • Conda + version: 1.30.0
  • EDAM operation (no superclasses): + Variant calling, DNA barcoding
  • EDAM topic (no superclasses): + Sequencing, Genetic variation, Microbial ecology, Metagenomics
  • Available + on UseGalaxy.org (Main): 10
  • Available on UseGalaxy.org.au: + 10
  • Available on UseGalaxy.eu: 10
  • Available + on UseGalaxy.fr: 10
  • Tools available on UseGalaxy.org (Main): + 10
  • Tools available on UseGalaxy.org.au: 10
  • Tools + available on UseGalaxy.eu: 10
  • Tools available on UseGalaxy.fr: + 10
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 10
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 92240
  • No. of tool + users (all time) (usegalaxy.eu): 92240
  • Tool usage (5 years) + (usegalaxy.eu): 2716
  • Tool usage (all time) (usegalaxy.eu): + 2716
  • No. of tool users (5 years) (usegalaxy.org): 179176
  • No. + of tool users (all time) (usegalaxy.org): 179176
  • Tool usage + (5 years) (usegalaxy.org): 5317
  • Tool usage (all time) (usegalaxy.org): + 5317
  • No. of tool users (5 years) (usegalaxy.org.au): 12478
  • No. + of tool users (all time) (usegalaxy.org.au): 12478
  • Tool + usage (5 years) (usegalaxy.org.au): 394
  • Tool usage (all + time) (usegalaxy.org.au): 394
  • No. of tool users (5 years) + - all main servers: 283894
  • No. of tool users (all time) + - all main servers: 283894
  • Tool usage (5 years) - all main + servers: 8427
  • Tool usage (all time) - all main servers: + 8427
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: dada2 + - description_md: '
  • Galaxy tool ids: Fasta_to_Contig2Bin, das_tool
  • Description: + DAS Tool for genome resolved metagenomics
  • bio.tool id: + dastool
  • bio.tool ids: dastool
  • biii: + nan
  • bio.tool name: dastool
  • 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.
  • EDAM operation: Read binning
  • EDAM + topic: Metagenomics
  • Status: Up-to-date
  • Source: + https://github.com/cmks/DAS_Tool
  • ToolShed categories: Metagenomics
  • ToolShed + id: das_tool
  • Date of first commit of the suite: + 2022-06-23
  • Galaxy wrapper owner: iuc
  • Galaxy + wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool
  • Galaxy + wrapper version: 1.1.7
  • Conda id: das_tool
  • Conda + version: 1.1.7
  • EDAM operation (no superclasses): + Read binning
  • EDAM topic (no superclasses): Metagenomics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1323
  • No. of tool + users (all time) (usegalaxy.eu): 1323
  • Tool usage (5 years) + (usegalaxy.eu): 47
  • Tool usage (all time) (usegalaxy.eu): + 47
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1323
  • No. + of tool users (all time) - all main servers: 1323
  • Tool + usage (5 years) - all main servers: 47
  • Tool usage (all + time) - all main servers: 47
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: das_tool + - description_md: '
  • Galaxy tool ids: deseq2
  • Description: + Differential gene expression analysis based on the negative binomial distribution
  • bio.tool + id: DESeq2
  • bio.tool ids: DESeq2
  • biii: + nan
  • bio.tool name: DESeq2
  • 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.
  • EDAM + operation: Differential gene expression analysis, RNA-Seq analysis
  • EDAM + topic: RNA-Seq
  • Status: To update
  • Source: + https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
  • ToolShed + categories: Transcriptomics, RNA, Statistics
  • ToolShed id: + deseq2
  • Date of first commit of the suite: 2018-11-15
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2
  • Galaxy + wrapper version: 2.11.40.8
  • Conda id: bioconductor-deseq2
  • Conda + version: 1.42.0
  • EDAM operation (no superclasses): + Differential gene expression analysis, RNA-Seq analysis
  • EDAM topic + (no superclasses): RNA-Seq
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 97434
  • No. of tool users (all time) (usegalaxy.eu): 109474
  • Tool + usage (5 years) (usegalaxy.eu): 11355
  • Tool usage (all time) + (usegalaxy.eu): 12514
  • No. of tool users (5 years) (usegalaxy.org): + 183905
  • No. of tool users (all time) (usegalaxy.org): 246475
  • Tool + usage (5 years) (usegalaxy.org): 24951
  • Tool usage (all + time) (usegalaxy.org): 31957
  • No. of tool users (5 years) + (usegalaxy.org.au): 18551
  • No. of tool users (all time) + (usegalaxy.org.au): 20166
  • Tool usage (5 years) (usegalaxy.org.au): + 2647
  • Tool usage (all time) (usegalaxy.org.au): 2905
  • No. + of tool users (5 years) - all main servers: 299890
  • No. + of tool users (all time) - all main servers: 376115
  • Tool + usage (5 years) - all main servers: 38953
  • Tool usage (all + time) - all main servers: 47376
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: deseq2 + - description_md: '
  • Galaxy tool ids: bg_diamond, bg_diamond_makedb, + bg_diamond_view
  • Description: DIAMOND is a new alignment + tool for aligning short DNA sequencing reads to a protein reference database + such as NCBI-NR.
  • bio.tool id: diamond
  • bio.tool + ids: diamond
  • biii: nan
  • bio.tool name: + Diamond
  • 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.
  • EDAM operation: + Sequence alignment analysis
  • EDAM topic: Sequence analysis, + Proteins
  • Status: To update
  • Source: + https://github.com/bbuchfink/diamond
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: diamond
  • Date + of first commit of the suite: 2021-03-21
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond
  • Galaxy + wrapper version: 2.0.15
  • Conda id: diamond
  • Conda + version: 2.1.10
  • EDAM operation (no superclasses): + Sequence alignment analysis
  • EDAM topic (no superclasses): + Sequence analysis, Proteins
  • Available on UseGalaxy.org (Main): + 3
  • Available on UseGalaxy.org.au: 3
  • Available + on UseGalaxy.eu: 3
  • Available on UseGalaxy.fr: 3
  • Tools + available on UseGalaxy.org (Main): 3
  • Tools available on + UseGalaxy.org.au: 3
  • Tools available on UseGalaxy.eu: + 3
  • Tools available on UseGalaxy.fr: 3
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 61376
  • No. of tool users (all time) (usegalaxy.eu): 61746
  • Tool + usage (5 years) (usegalaxy.eu): 1847
  • Tool usage (all time) + (usegalaxy.eu): 1895
  • No. of tool users (5 years) (usegalaxy.org): + 23164
  • No. of tool users (all time) (usegalaxy.org): 28729
  • Tool + usage (5 years) (usegalaxy.org): 1140
  • Tool usage (all time) + (usegalaxy.org): 1556
  • No. of tool users (5 years) (usegalaxy.org.au): + 63034
  • No. of tool users (all time) (usegalaxy.org.au): + 63034
  • Tool usage (5 years) (usegalaxy.org.au): 522
  • Tool + usage (all time) (usegalaxy.org.au): 522
  • No. of tool users + (5 years) - all main servers: 147574
  • No. of tool users + (all time) - all main servers: 153509
  • Tool usage (5 years) + - all main servers: 3509
  • Tool usage (all time) - all main + servers: 3973
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: diamond + - description_md: '
  • Galaxy tool ids: disco
  • Description: + DISCO is a overlap-layout-consensus (OLC) metagenome assembler
  • bio.tool + id: disco
  • bio.tool ids: disco
  • biii: + nan
  • bio.tool name: DISCO
  • 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.
  • EDAM operation: Protein sequence + analysis
  • EDAM topic: Structure determination
  • Status: + To update
  • Source: http://disco.omicsbio.org/
  • ToolShed + categories: Metagenomics, Assembly
  • ToolShed id: + disco
  • Date of first commit of the suite: 2017-10-26
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco
  • Galaxy + wrapper version: nan
  • Conda id: disco
  • Conda + version: 1.2
  • EDAM operation (no superclasses): Protein + sequence analysis
  • EDAM topic (no superclasses): Structure + determination
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 358
  • No. of tool + users (all time) (usegalaxy.eu): 406
  • Tool usage (5 years) + (usegalaxy.eu): 124
  • Tool usage (all time) (usegalaxy.eu): + 139
  • No. of tool users (5 years) (usegalaxy.org): 1361
  • No. + of tool users (all time) (usegalaxy.org): 1361
  • Tool usage + (5 years) (usegalaxy.org): 384
  • Tool usage (all time) (usegalaxy.org): + 384
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1719
  • No. + of tool users (all time) - all main servers: 1767
  • Tool + usage (5 years) - all main servers: 508
  • Tool usage (all + time) - all main servers: 523
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: disco + - description_md: '
  • Galaxy tool ids: dram_annotate, dram_distill, + dram_merge_annotations, dram_neighborhoods, dram_strainer
  • Description: + DRAM for distilling microbial metabolism to automate the curation of microbiome + function
  • bio.tool id: dram
  • bio.tool ids: + dram
  • biii: nan
  • bio.tool name: DRAM
  • bio.tool + description: Distilled and Refined Annotation of Metabolism: A tool for + the annotation and curation of function for microbial and viral genomes
  • EDAM + operation: Gene functional annotation
  • EDAM topic: + Metagenomics, Biological databases, Molecular genetics
  • Status: + Up-to-date
  • Source: https://github.com/WrightonLabCSU/DRAM
  • ToolShed + categories: Metagenomics
  • ToolShed id: dram
  • Date + of first commit of the suite: 2022-09-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram
  • Galaxy + wrapper version: 1.5.0
  • Conda id: dram
  • Conda + version: 1.5.0
  • EDAM operation (no superclasses): + Gene functional annotation
  • EDAM topic (no superclasses): + Metagenomics, Biological databases, Molecular genetics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 5
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 7358
  • No. of tool + users (all time) (usegalaxy.eu): 7358
  • Tool usage (5 years) + (usegalaxy.eu): 88
  • Tool usage (all time) (usegalaxy.eu): + 88
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 7358
  • No. + of tool users (all time) - all main servers: 7358
  • Tool + usage (5 years) - all main servers: 88
  • Tool usage (all + time) - all main servers: 88
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: dram + - description_md: '
  • Galaxy tool ids: drep_compare, drep_dereplicate
  • Description: + dRep compares and dereplicates genome sets
  • bio.tool id: + drep
  • bio.tool ids: drep
  • biii: nan
  • bio.tool + name: dRep
  • bio.tool description: Fast and accurate + genomic comparisons that enables improved genome recovery from metagenomes through + de-replication.
  • EDAM operation: Genome comparison
  • EDAM + topic: Metagenomics, Genomics, Sequence analysis
  • Status: + Up-to-date
  • Source: https://github.com/MrOlm/drep
  • ToolShed + categories: Metagenomics
  • ToolShed id: drep
  • Date + of first commit of the suite: 2020-01-06
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep
  • Galaxy + wrapper version: 3.5.0
  • Conda id: drep
  • Conda + version: 3.5.0
  • EDAM operation (no superclasses): + Genome comparison
  • EDAM topic (no superclasses): Metagenomics, + Sequence analysis
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 2
  • Available on UseGalaxy.fr: 2
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 2
  • Tools + available on UseGalaxy.fr: 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: + 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 916
  • No. of tool + users (all time) (usegalaxy.eu): 916
  • Tool usage (5 years) + (usegalaxy.eu): 113
  • Tool usage (all time) (usegalaxy.eu): + 113
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 916
  • No. + of tool users (all time) - all main servers: 916
  • Tool usage + (5 years) - all main servers: 113
  • Tool usage (all time) + - all main servers: 113
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: drep + - description_md: '
  • Galaxy tool ids: ectyper
  • Description: + EC-Typer - in silico serotyping of Escherichia coli species
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: Up-to-date
  • Source: https://github.com/phac-nml/ecoli_serotyping
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: ectyper
  • Date + of first commit of the suite: 2018-12-21
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/ecoli_serotyping
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper
  • Galaxy + wrapper version: 1.0.0
  • Conda id: ectyper
  • Conda + version: 1.0.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 12996
  • No. of tool + users (all time) (usegalaxy.eu): 12996
  • Tool usage (5 years) + (usegalaxy.eu): 137
  • Tool usage (all time) (usegalaxy.eu): + 137
  • No. of tool users (5 years) (usegalaxy.org): 10
  • No. + of tool users (all time) (usegalaxy.org): 10
  • Tool usage + (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): + 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 13006
  • No. + of tool users (all time) - all main servers: 13006
  • Tool + usage (5 years) - all main servers: 138
  • Tool usage (all + time) - all main servers: 138
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: ectyper + - description_md: '
  • Galaxy tool ids: effectiveT3
  • Description: + Find bacterial type III effectors in protein sequences
  • bio.tool + id: effectivet3
  • bio.tool ids: effectivet3
  • biii: + nan
  • bio.tool name: EffectiveT3
  • bio.tool description: + Prediction of putative Type-III secreted proteins.
  • EDAM operation: + Sequence classification
  • EDAM topic: Sequence analysis
  • Status: + To update
  • Source: http://effectors.org
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: effectivet3
  • Date + of first commit of the suite: 2015-09-21
  • Galaxy wrapper + owner: peterjc
  • Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
  • Galaxy + wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
  • Galaxy + wrapper version: 0.0.21
  • Conda id: effectiveT3
  • Conda + version: 1.0.1
  • EDAM operation (no superclasses): + Sequence classification
  • EDAM topic (no superclasses): Sequence + analysis
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 0
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 0
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: effectiveT3 + - description_md: '
  • Galaxy tool ids: eggnog_mapper, eggnog_mapper_annotate, + eggnog_mapper_search
  • Description: eggnog-mapper fast functional + annotation of novel sequences
  • bio.tool id: eggnog-mapper-v2
  • bio.tool + ids: eggnog-mapper-v2
  • biii: nan
  • bio.tool + name: eggNOG-mapper v2
  • bio.tool description: EggNOG-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.
  • EDAM + operation: Homology-based gene prediction, Genome annotation, Fold recognition, + Information extraction, Query and retrieval
  • EDAM topic: + Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis
  • Status: + To update
  • Source: nan
  • ToolShed categories: + Proteomics
  • ToolShed id: eggnog_mapper
  • Date + of first commit of the suite: 2019-11-11
  • Galaxy wrapper + owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper
  • Galaxy + wrapper version: 2.1.8
  • Conda id: eggnog-mapper
  • Conda + version: 2.1.12
  • EDAM operation (no superclasses): + Homology-based gene prediction, Genome annotation, Fold recognition, Information + extraction, Query and retrieval
  • EDAM topic (no superclasses): + Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis
  • Available + on UseGalaxy.org (Main): 3
  • Available on UseGalaxy.org.au: + 3
  • Available on UseGalaxy.eu: 3
  • Available + on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): + 3
  • Tools available on UseGalaxy.org.au: 3
  • Tools + available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: + 3
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 3
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 3
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 34432
  • No. of tool + users (all time) (usegalaxy.eu): 34437
  • Tool usage (5 years) + (usegalaxy.eu): 1149
  • Tool usage (all time) (usegalaxy.eu): + 1152
  • No. of tool users (5 years) (usegalaxy.org): 42
  • No. + of tool users (all time) (usegalaxy.org): 42
  • Tool usage + (5 years) (usegalaxy.org): 2
  • Tool usage (all time) (usegalaxy.org): + 2
  • No. of tool users (5 years) (usegalaxy.org.au): 21027
  • No. + of tool users (all time) (usegalaxy.org.au): 21027
  • Tool + usage (5 years) (usegalaxy.org.au): 413
  • Tool usage (all + time) (usegalaxy.org.au): 413
  • No. of tool users (5 years) + - all main servers: 55501
  • No. of tool users (all time) + - all main servers: 55506
  • Tool usage (5 years) - all main + servers: 1564
  • Tool usage (all time) - all main servers: + 1567
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: eggnog_mapper + - description_md: '
  • 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
  • Description: + Galaxy wrappers for EMBOSS version 5.0.0 tools
  • bio.tool id: + emboss
  • bio.tool ids: emboss
  • biii: + nan
  • bio.tool name: EMBOSS
  • bio.tool description: + Diverse suite of tools for sequence analysis; many programs analagous to GCG; + context-sensitive help for each tool.
  • EDAM operation: Sequence + analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence + alignment
  • EDAM topic: Molecular biology, Sequence analysis, + Biology
  • Status: To update
  • Source: + http://emboss.open-bio.org/
  • ToolShed categories: Sequence + Analysis, Fasta Manipulation
  • ToolShed id: emboss_5
  • Date + of first commit of the suite: 2017-01-11
  • Galaxy wrapper + owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5
  • Galaxy + wrapper version: 5.0.0
  • Conda id: emboss
  • Conda + version: 6.6.0
  • EDAM operation (no superclasses): + Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, + Sequence alignment
  • EDAM topic (no superclasses): Molecular + biology, Sequence analysis
  • Available on UseGalaxy.org (Main): + 107
  • Available on UseGalaxy.org.au: 107
  • Available + on UseGalaxy.eu: 107
  • Available on UseGalaxy.fr: + 107
  • Tools available on UseGalaxy.org (Main): 107
  • Tools + available on UseGalaxy.org.au: 107
  • Tools available on UseGalaxy.eu: + 107
  • Tools available on UseGalaxy.fr: 107
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 107
  • Tools available on Viral + Variant Visualizer (VVV): 0
  • No. of tool users (5 years) + (usegalaxy.eu): 143762
  • No. of tool users (all time) (usegalaxy.eu): + 148864
  • Tool usage (5 years) (usegalaxy.eu): 4481
  • Tool + usage (all time) (usegalaxy.eu): 5039
  • No. of tool users + (5 years) (usegalaxy.org): 151989
  • No. of tool users (all + time) (usegalaxy.org): 296028
  • Tool usage (5 years) (usegalaxy.org): + 13224
  • Tool usage (all time) (usegalaxy.org): 31140
  • No. + of tool users (5 years) (usegalaxy.org.au): 24955
  • No. of + tool users (all time) (usegalaxy.org.au): 27001
  • Tool usage + (5 years) (usegalaxy.org.au): 2397
  • Tool usage (all time) + (usegalaxy.org.au): 2705
  • No. of tool users (5 years) - + all main servers: 320706
  • No. of tool users (all time) - + all main servers: 471893
  • Tool usage (5 years) - all main + servers: 20102
  • Tool usage (all time) - all main servers: + 38884
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: emboss_5 + - description_md: '
  • 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
  • Description: + Analyse phylogenetic trees using the ETE Toolkit
  • bio.tool id: + ete
  • bio.tool ids: ete
  • biii: nan
  • bio.tool + name: ete
  • 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
  • EDAM operation: + Phylogenetic analysis, Phylogenetic tree editing
  • EDAM topic: + Phylogenetics
  • Status: To update
  • Source: + http://etetoolkit.org/
  • ToolShed categories: Phylogenetics
  • ToolShed + id: ete
  • Date of first commit of the suite: 2018-10-11
  • Galaxy + wrapper owner: earlhaminst
  • Galaxy wrapper source: + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete
  • Galaxy + wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete
  • Galaxy + wrapper version: 3.1.2
  • Conda id: ete3
  • Conda + version: 3.1.1
  • EDAM operation (no superclasses): + Phylogenetic tree editing
  • EDAM topic (no superclasses): + Phylogenetics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 7
  • Available on UseGalaxy.fr: 7
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 7
  • Tools + available on UseGalaxy.fr: 7
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 7
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 820
  • No. of tool + users (all time) (usegalaxy.eu): 966
  • Tool usage (5 years) + (usegalaxy.eu): 89
  • Tool usage (all time) (usegalaxy.eu): + 106
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 820
  • No. + of tool users (all time) - all main servers: 966
  • Tool usage + (5 years) - all main servers: 89
  • Tool usage (all time) + - all main servers: 106
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: ete + - description_md: '
  • Galaxy tool ids: export2graphlan
  • Description: + export2graphlan is a conversion software tool for producing both annotation + and tree file for GraPhlAn
  • bio.tool id: export2graphlan
  • bio.tool + ids: export2graphlan
  • biii: nan
  • bio.tool + name: export2graphlan
  • 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.
  • EDAM + operation: Conversion
  • EDAM topic: Taxonomy, Metabolomics, + Biomarkers
  • Status: To update
  • Source: + https://bitbucket.org/CibioCM/export2graphlan/overview
  • ToolShed + categories: Metagenomics
  • ToolShed id: export2graphlan
  • Date + of first commit of the suite: 2017-03-03
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan
  • Galaxy + wrapper version: 0.20
  • Conda id: export2graphlan
  • Conda + version: 0.22
  • EDAM operation (no superclasses): + Conversion
  • EDAM topic (no superclasses): Taxonomy, Metabolomics, + Biomarkers
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 5396
  • No. of tool + users (all time) (usegalaxy.eu): 5938
  • Tool usage (5 years) + (usegalaxy.eu): 580
  • Tool usage (all time) (usegalaxy.eu): + 607
  • No. of tool users (5 years) (usegalaxy.org): 628
  • No. + of tool users (all time) (usegalaxy.org): 628
  • Tool usage + (5 years) (usegalaxy.org): 168
  • Tool usage (all time) (usegalaxy.org): + 168
  • No. of tool users (5 years) (usegalaxy.org.au): 519
  • No. + of tool users (all time) (usegalaxy.org.au): 519
  • Tool usage + (5 years) (usegalaxy.org.au): 107
  • Tool usage (all time) + (usegalaxy.org.au): 107
  • No. of tool users (5 years) - all + main servers: 6543
  • No. of tool users (all time) - all main + servers: 7085
  • Tool usage (5 years) - all main servers: + 855
  • Tool usage (all time) - all main servers: 882
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: export2graphlan + - description_md: '
  • Galaxy tool ids: ez_histograms
  • Description: + ggplot2 histograms and density plots
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://github.com/tidyverse/ggplot2
  • ToolShed categories: + Visualization, Statistics
  • ToolShed id: ez_histograms
  • Date + of first commit of the suite: 2024-02-07
  • Galaxy wrapper + owner: artbio
  • Galaxy wrapper source: https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms
  • Galaxy + wrapper parsed folder: https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms
  • Galaxy + wrapper version: 3.4.4
  • Conda id: r-ggplot2
  • Conda + version: 2.2.1
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: ez_histograms + - description_md: '
  • Galaxy tool ids: fargene
  • Description: + fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )
  • bio.tool + id: fargene
  • bio.tool ids: fargene
  • biii: + nan
  • bio.tool name: fARGene
  • 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.
  • EDAM + operation: Antimicrobial resistance prediction
  • EDAM topic: + Metagenomics, Microbiology, Public health and epidemiology
  • Status: + Up-to-date
  • Source: https://github.com/fannyhb/fargene
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: fargene
  • Date + of first commit of the suite: 2019-08-30
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene
  • Galaxy + wrapper version: 0.1
  • Conda id: fargene
  • Conda + version: 0.1
  • EDAM operation (no superclasses): Antimicrobial + resistance prediction
  • EDAM topic (no superclasses): Metagenomics, + Microbiology, Public health and epidemiology
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 601
  • No. of tool users (all time) (usegalaxy.eu): 601
  • Tool + usage (5 years) (usegalaxy.eu): 128
  • Tool usage (all time) + (usegalaxy.eu): 128
  • No. of tool users (5 years) (usegalaxy.org): + 1165
  • No. of tool users (all time) (usegalaxy.org): 1165
  • Tool + usage (5 years) (usegalaxy.org): 232
  • Tool usage (all time) + (usegalaxy.org): 232
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 1766
  • No. of tool users (all time) - all main + servers: 1766
  • Tool usage (5 years) - all main servers: + 360
  • Tool usage (all time) - all main servers: 360
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: fargene + - description_md: '
  • Galaxy tool ids: fastani
  • Description: + Fast alignment-free computation of whole-genome Average Nucleotide Identity
  • bio.tool + id: fastani
  • bio.tool ids: fastani
  • biii: + nan
  • bio.tool name: FastANI
  • 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.
  • EDAM operation: + Genome alignment, Sequence similarity search
  • EDAM topic: + Microbiology, Genetic variation
  • Status: To update
  • Source: + https://github.com/ParBLiSS/FastANI
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: fastani
  • Date + of first commit of the suite: 2020-02-17
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani
  • Galaxy + wrapper version: 1.3
  • Conda id: fastani
  • Conda + version: 1.34
  • EDAM operation (no superclasses): + Genome alignment, Sequence similarity search
  • EDAM topic (no superclasses): + Microbiology, Genetic variation
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 6685
  • No. of tool users (all time) (usegalaxy.eu): 6685
  • Tool + usage (5 years) (usegalaxy.eu): 603
  • Tool usage (all time) + (usegalaxy.eu): 603
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 6685
  • No. of tool users (all time) - all main + servers: 6685
  • Tool usage (5 years) - all main servers: + 603
  • Tool usage (all time) - all main servers: 603
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: fastani + - description_md: '
  • Galaxy tool ids: fastk_fastk
  • Description: + FastK: A K-mer counter (for HQ assembly data sets)
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: https://github.com/thegenemyers/FASTK
  • ToolShed + categories: Assembly
  • ToolShed id: fastk
  • Date + of first commit of the suite: 2024-05-03
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk
  • Galaxy + wrapper version: 1.0.0
  • Conda id: fastk
  • Conda + version: 1.0
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 136
  • No. of tool users (all time) (usegalaxy.eu): 136
  • Tool + usage (5 years) (usegalaxy.eu): 11
  • Tool usage (all time) + (usegalaxy.eu): 11
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 136
  • No. of tool users (all time) - all main + servers: 136
  • Tool usage (5 years) - all main servers: + 11
  • Tool usage (all time) - all main servers: 11
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: fastk + - description_md: '
  • Galaxy tool ids: fastp
  • Description: + Fast all-in-one preprocessing for FASTQ files
  • bio.tool id: + fastp
  • bio.tool ids: fastp
  • biii: nan
  • bio.tool + name: fastp
  • 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.
  • EDAM + operation: Sequencing quality control, Sequence contamination filtering
  • EDAM + topic: Sequence analysis, Probes and primers
  • Status: + Up-to-date
  • Source: https://github.com/OpenGene/fastp
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: fastp
  • Date + of first commit of the suite: 2018-03-18
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp
  • Galaxy + wrapper version: 0.23.4
  • Conda id: fastp
  • Conda + version: 0.23.4
  • EDAM operation (no superclasses): + Sequence contamination filtering
  • EDAM topic (no superclasses): + Probes and primers
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 1
  • No. + of tool users (5 years) (usegalaxy.eu): 1126086
  • No. of + tool users (all time) (usegalaxy.eu): 1127111
  • Tool usage + (5 years) (usegalaxy.eu): 6847
  • Tool usage (all time) (usegalaxy.eu): + 6909
  • No. of tool users (5 years) (usegalaxy.org): 422259
  • No. + of tool users (all time) (usegalaxy.org): 422259
  • Tool usage + (5 years) (usegalaxy.org): 10722
  • Tool usage (all time) + (usegalaxy.org): 10722
  • No. of tool users (5 years) (usegalaxy.org.au): + 76462
  • No. of tool users (all time) (usegalaxy.org.au): + 76462
  • Tool usage (5 years) (usegalaxy.org.au): 2242
  • Tool + usage (all time) (usegalaxy.org.au): 2242
  • No. of tool users + (5 years) - all main servers: 1624807
  • No. of tool users + (all time) - all main servers: 1625832
  • Tool usage (5 years) + - all main servers: 19811
  • Tool usage (all time) - all main + servers: 19873
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: fastp + - description_md: '
  • Galaxy tool ids: fastqe
  • Description: + FASTQE
  • bio.tool id: fastqe
  • bio.tool ids: + fastqe
  • biii: nan
  • bio.tool name: FASTQE
  • bio.tool + description: Compute quality stats for FASTQ files and print those stats + as emoji... for some reason.
  • EDAM operation: Sequencing + quality control
  • EDAM topic: Sequence analysis, Sequencing
  • Status: + To update
  • Source: https://fastqe.com/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: fastqe
  • Date + of first commit of the suite: 2020-07-13
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe
  • Galaxy + wrapper version: 0.3.1+galaxy0
  • Conda id: fastqe
  • Conda + version: 0.3.1
  • EDAM operation (no superclasses): + Sequencing quality control
  • EDAM topic (no superclasses): + Sequence analysis, Sequencing
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 5162
  • No. of tool users (all time) (usegalaxy.eu): 5162
  • Tool + usage (5 years) (usegalaxy.eu): 2350
  • Tool usage (all time) + (usegalaxy.eu): 2350
  • No. of tool users (5 years) (usegalaxy.org): + 10176
  • No. of tool users (all time) (usegalaxy.org): 10176
  • Tool + usage (5 years) (usegalaxy.org): 4714
  • Tool usage (all time) + (usegalaxy.org): 4714
  • No. of tool users (5 years) (usegalaxy.org.au): + 2610
  • No. of tool users (all time) (usegalaxy.org.au): 2610
  • Tool + usage (5 years) (usegalaxy.org.au): 991
  • Tool usage (all + time) (usegalaxy.org.au): 991
  • No. of tool users (5 years) + - all main servers: 17948
  • No. of tool users (all time) + - all main servers: 17948
  • Tool usage (5 years) - all main + servers: 8055
  • Tool usage (all time) - all main servers: + 8055
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: fastqe + - description_md: '
  • Galaxy tool ids: fasttree
  • Description: + FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments + of nucleotide or protein sequences - GVL
  • bio.tool id: fasttree
  • bio.tool + ids: fasttree
  • biii: nan
  • bio.tool name: + FastTree
  • bio.tool description: Infers approximately-maximum-likelihood + phylogenetic trees from alignments of nucleotide or protein sequences.
  • EDAM + operation: Phylogenetic tree generation (from molecular sequences), Phylogenetic + tree generation (maximum likelihood and Bayesian methods)
  • EDAM + topic: Phylogenetics, Sequence analysis
  • Status: + To update
  • Source: http://www.microbesonline.org/fasttree/
  • ToolShed + categories: Phylogenetics
  • ToolShed id: fasttree
  • Date + of first commit of the suite: 2018-02-02
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree
  • Galaxy + wrapper version: 2.1.10
  • Conda id: fasttree
  • Conda + version: 2.1.11
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): Phylogenetics
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 65542
  • No. of tool + users (all time) (usegalaxy.eu): 65631
  • Tool usage (5 years) + (usegalaxy.eu): 1049
  • Tool usage (all time) (usegalaxy.eu): + 1071
  • No. of tool users (5 years) (usegalaxy.org): 25992
  • No. + of tool users (all time) (usegalaxy.org): 25992
  • Tool usage + (5 years) (usegalaxy.org): 2147
  • Tool usage (all time) (usegalaxy.org): + 2147
  • No. of tool users (5 years) (usegalaxy.org.au): 6733
  • No. + of tool users (all time) (usegalaxy.org.au): 7339
  • Tool + usage (5 years) (usegalaxy.org.au): 649
  • Tool usage (all + time) (usegalaxy.org.au): 745
  • No. of tool users (5 years) + - all main servers: 98267
  • No. of tool users (all time) + - all main servers: 98962
  • Tool usage (5 years) - all main + servers: 3845
  • Tool usage (all time) - all main servers: + 3963
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: fasttree + - description_md: '
  • Galaxy tool ids: featurecounts
  • Description: + featureCounts counts the number of reads aligned to defined masked regions in + a reference genome
  • bio.tool id: featurecounts
  • bio.tool + ids: featurecounts
  • biii: nan
  • bio.tool + name: FeatureCounts
  • 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.
  • EDAM operation: + Read summarisation, RNA-Seq quantification
  • EDAM topic: + RNA-Seq
  • Status: To update
  • Source: + http://bioinf.wehi.edu.au/featureCounts
  • ToolShed categories: + RNA, Transcriptomics, Sequence Analysis
  • ToolShed id: featurecounts
  • Date + of first commit of the suite: 2019-05-28
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts
  • Galaxy + wrapper version: 2.0.3
  • Conda id: subread
  • Conda + version: 2.0.6
  • EDAM operation (no superclasses): + Read summarisation, RNA-Seq quantification
  • EDAM topic (no superclasses): + RNA-Seq
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 740719
  • No. of tool + users (all time) (usegalaxy.eu): 770524
  • Tool usage (5 years) + (usegalaxy.eu): 11699
  • Tool usage (all time) (usegalaxy.eu): + 12547
  • No. of tool users (5 years) (usegalaxy.org): 643892
  • No. + of tool users (all time) (usegalaxy.org): 784396
  • Tool usage + (5 years) (usegalaxy.org): 23272
  • Tool usage (all time) + (usegalaxy.org): 27598
  • No. of tool users (5 years) (usegalaxy.org.au): + 66108
  • No. of tool users (all time) (usegalaxy.org.au): + 68867
  • Tool usage (5 years) (usegalaxy.org.au): 2348
  • Tool + usage (all time) (usegalaxy.org.au): 2463
  • No. of tool users + (5 years) - all main servers: 1450719
  • No. of tool users + (all time) - all main servers: 1623787
  • Tool usage (5 years) + - all main servers: 37319
  • Tool usage (all time) - all main + servers: 42608
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: featurecounts + - description_md: '
  • Galaxy tool ids: filter_spades_repeat
  • Description: + Remove short and repeat contigs/scaffolds
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: https://github.com/phac-nml/galaxy_tools/
  • ToolShed + categories: Assembly
  • ToolShed id: filter_spades_repeats
  • Date + of first commit of the suite: 2017-10-12
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools/
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats
  • Galaxy + wrapper version: 1.0.1
  • Conda id: perl-bioperl
  • Conda + version: 1.7.8
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: filter_spades_repeats + - description_md: '
  • Galaxy tool ids: filtlong
  • Description: + Filtlong - Filtering long reads by quality
  • bio.tool id: + filtlong
  • bio.tool ids: filtlong
  • biii: + nan
  • bio.tool name: Filtlong
  • 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.
  • EDAM operation: Filtering, Sequencing quality + control
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: + https://github.com/rrwick/Filtlong
  • ToolShed categories: + Fastq Manipulation, Sequence Analysis
  • ToolShed id: filtlong
  • Date + of first commit of the suite: 2018-09-14
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong
  • Galaxy + wrapper version: 0.2.1
  • Conda id: filtlong
  • Conda + version: 0.2.1
  • EDAM operation (no superclasses): + Filtering, Sequencing quality control
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 53310
  • No. of tool + users (all time) (usegalaxy.eu): 53944
  • Tool usage (5 years) + (usegalaxy.eu): 1499
  • Tool usage (all time) (usegalaxy.eu): + 1575
  • No. of tool users (5 years) (usegalaxy.org): 25043
  • No. + of tool users (all time) (usegalaxy.org): 25043
  • Tool usage + (5 years) (usegalaxy.org): 726
  • Tool usage (all time) (usegalaxy.org): + 726
  • No. of tool users (5 years) (usegalaxy.org.au): 10824
  • No. + of tool users (all time) (usegalaxy.org.au): 10824
  • Tool + usage (5 years) (usegalaxy.org.au): 593
  • Tool usage (all + time) (usegalaxy.org.au): 593
  • No. of tool users (5 years) + - all main servers: 89177
  • No. of tool users (all time) + - all main servers: 89811
  • Tool usage (5 years) - all main + servers: 2818
  • Tool usage (all time) - all main servers: + 2894
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: filtlong + - description_md: '
  • Galaxy tool ids: flashlfq
  • Description: + FlashLFQ mass-spectrometry proteomics label-free quantification
  • bio.tool + id: flashlfq
  • bio.tool ids: flashlfq
  • biii: + nan
  • bio.tool name: FlashLFQ
  • bio.tool description: + FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry + proteomics.
  • EDAM operation: Label-free quantification
  • EDAM + topic: Proteomics experiment, Proteomics
  • Status: + To update
  • Source: https://github.com/smith-chem-wisc/FlashLFQ
  • ToolShed + categories: Proteomics
  • ToolShed id: flashlfq
  • Date + of first commit of the suite: 2017-12-06
  • Galaxy wrapper + owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq
  • Galaxy + wrapper version: 1.0.3.1
  • Conda id: flashlfq
  • Conda + version: 1.2.6
  • EDAM operation (no superclasses): + Label-free quantification
  • EDAM topic (no superclasses): + Proteomics experiment, Proteomics
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 661
  • No. of tool users (all time) (usegalaxy.eu): 715
  • Tool + usage (5 years) (usegalaxy.eu): 52
  • Tool usage (all time) + (usegalaxy.eu): 54
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 167
  • No. of tool users (all time) (usegalaxy.org.au): 167
  • Tool + usage (5 years) (usegalaxy.org.au): 15
  • Tool usage (all + time) (usegalaxy.org.au): 15
  • No. of tool users (5 years) + - all main servers: 828
  • No. of tool users (all time) - + all main servers: 882
  • Tool usage (5 years) - all main servers: + 67
  • Tool usage (all time) - all main servers: 69
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: flashlfq + - description_md: '
  • Galaxy tool ids: flye
  • Description: + Assembly of long and error-prone reads.
  • bio.tool id: Flye
  • bio.tool + ids: Flye
  • biii: nan
  • bio.tool name: + Flye
  • 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.
  • EDAM operation: Genome assembly, De-novo assembly, + Mapping assembly, Cross-assembly
  • EDAM topic: Sequence assembly, + Metagenomics, Whole genome sequencing, Genomics
  • Status: + Up-to-date
  • Source: https://github.com/fenderglass/Flye/
  • ToolShed + categories: Assembly
  • ToolShed id: flye
  • Date + of first commit of the suite: 2018-09-24
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/flye
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/flye
  • Galaxy + wrapper version: 2.9.5
  • Conda id: flye
  • Conda + version: 2.9.5
  • EDAM operation (no superclasses): + Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly
  • EDAM + topic (no superclasses): Sequence assembly, Metagenomics, Whole genome + sequencing
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 32514
  • No. of tool + users (all time) (usegalaxy.eu): 32675
  • Tool usage (5 years) + (usegalaxy.eu): 3379
  • Tool usage (all time) (usegalaxy.eu): + 3422
  • No. of tool users (5 years) (usegalaxy.org): 19434
  • No. + of tool users (all time) (usegalaxy.org): 19434
  • Tool usage + (5 years) (usegalaxy.org): 2537
  • Tool usage (all time) (usegalaxy.org): + 2537
  • No. of tool users (5 years) (usegalaxy.org.au): 9843
  • No. + of tool users (all time) (usegalaxy.org.au): 9843
  • Tool + usage (5 years) (usegalaxy.org.au): 1624
  • Tool usage (all + time) (usegalaxy.org.au): 1624
  • No. of tool users (5 years) + - all main servers: 61791
  • No. of tool users (all time) + - all main servers: 61952
  • Tool usage (5 years) - all main + servers: 7540
  • Tool usage (all time) - all main servers: + 7583
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: flye + - description_md: '
  • Galaxy tool ids: format_metaphlan2_output
  • Description: + Format MetaPhlAn2 output to extract abundance at different taxonomic levels
  • bio.tool + id: format_metaphlan2_output
  • bio.tool ids: format_metaphlan2_output
  • biii: + nan
  • bio.tool name: Format metaphlan2 output
  • bio.tool + description: This tool format output file of MetaPhlan2 containing community + content (abundance) at all taxonomic levels (from kingdom to strains).
  • EDAM + operation: Formatting
  • EDAM topic: Taxonomy, Metagenomics
  • Status: + To update
  • Source: nan
  • ToolShed categories: + Metagenomics
  • ToolShed id: format_metaphlan2_output
  • Date + of first commit of the suite: 2022-10-19
  • Galaxy wrapper + owner: bebatut
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output
  • Galaxy + wrapper version: 0.2.0
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): Formatting
  • EDAM + topic (no superclasses): Taxonomy, Metagenomics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 5940
  • No. of tool + users (all time) (usegalaxy.eu): 6474
  • Tool usage (5 years) + (usegalaxy.eu): 558
  • Tool usage (all time) (usegalaxy.eu): + 608
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 5940
  • No. + of tool users (all time) - all main servers: 6474
  • Tool + usage (5 years) - all main servers: 558
  • Tool usage (all + time) - all main servers: 608
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: format_metaphlan2_output + - description_md: '
  • Galaxy tool ids: fraggenescan
  • Description: + Tool for finding (fragmented) genes in short read
  • bio.tool id: + fraggenescan
  • bio.tool ids: fraggenescan
  • biii: + nan
  • bio.tool name: FragGeneScan
  • bio.tool + description: Application for finding (fragmented) genes in short reads
  • EDAM + operation: Gene prediction
  • EDAM topic: Genetics, + Sequence analysis
  • Status: To update
  • Source: + https://sourceforge.net/projects/fraggenescan/
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: fraggenescan
  • Date + of first commit of the suite: 2017-09-04
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan
  • Galaxy + wrapper version: nan
  • Conda id: fraggenescan
  • Conda + version: 1.31
  • EDAM operation (no superclasses): + Gene prediction
  • EDAM topic (no superclasses): Genetics, + Sequence analysis
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1257
  • No. of tool + users (all time) (usegalaxy.eu): 1450
  • Tool usage (5 years) + (usegalaxy.eu): 150
  • Tool usage (all time) (usegalaxy.eu): + 162
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 1052
  • No. + of tool users (all time) (usegalaxy.org.au): 1052
  • Tool + usage (5 years) (usegalaxy.org.au): 45
  • Tool usage (all + time) (usegalaxy.org.au): 45
  • No. of tool users (5 years) + - all main servers: 2309
  • No. of tool users (all time) - + all main servers: 2502
  • Tool usage (5 years) - all main + servers: 195
  • Tool usage (all time) - all main servers: + 207
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: fraggenescan + - description_md: '
  • Galaxy tool ids: freyja_aggregate_plot, + freyja_boot, freyja_demix, freyja_variants
  • Description: + lineage abundances estimation
  • bio.tool id: freyja
  • bio.tool + ids: freyja
  • biii: nan
  • bio.tool name: + Freyja
  • bio.tool description: Recover relative lineage abundances + from mixed SARS-CoV-2 samples from a sequencing dataset
  • EDAM operation: + RNA-Seq quantification
  • EDAM topic: Metagenomics
  • Status: + Up-to-date
  • Source: https://github.com/andersen-lab/Freyja
  • ToolShed + categories: Metagenomics, Sequence Analysis
  • ToolShed id: + freyja
  • Date of first commit of the suite: 2022-07-05
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja
  • Galaxy + wrapper version: 1.5.1
  • Conda id: freyja
  • Conda + version: 1.5.1
  • EDAM operation (no superclasses): + RNA-Seq quantification
  • EDAM topic (no superclasses): Metagenomics
  • Available + on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 4
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 2
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 4
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 21757
  • No. of tool + users (all time) (usegalaxy.eu): 21757
  • Tool usage (5 years) + (usegalaxy.eu): 101
  • Tool usage (all time) (usegalaxy.eu): + 101
  • No. of tool users (5 years) (usegalaxy.org): 217
  • No. + of tool users (all time) (usegalaxy.org): 217
  • Tool usage + (5 years) (usegalaxy.org): 21
  • Tool usage (all time) (usegalaxy.org): + 21
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 21974
  • No. + of tool users (all time) - all main servers: 21974
  • Tool + usage (5 years) - all main servers: 122
  • Tool usage (all + time) - all main servers: 122
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: freyja + - description_md: '
  • 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
  • Description: + Suite for metabarcoding analysis
  • bio.tool id: frogs
  • bio.tool + ids: frogs
  • biii: nan
  • bio.tool name: + FROGS
  • 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.
  • EDAM operation: + Taxonomic classification
  • EDAM topic: Metagenomics, Microbial + ecology, Taxonomy, Evolutionary biology, Sequencing
  • Status: + To update
  • Source: http://frogs.toulouse.inrae.fr/
  • ToolShed + categories: Metagenomics
  • ToolShed id: frogs
  • Date + of first commit of the suite: 2023-04-26
  • Galaxy wrapper + owner: frogs
  • Galaxy wrapper source: https://github.com/geraldinepascal/FROGS-wrappers/
  • Galaxy + wrapper parsed folder: https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs
  • Galaxy + wrapper version: 4.1.0
  • Conda id: frogs
  • Conda + version: 5.0.0
  • EDAM operation (no superclasses): + Taxonomic classification
  • EDAM topic (no superclasses): + Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 28
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 28
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: frogs + - description_md: '
  • Galaxy tool ids: funannotate_annotate, funannotate_clean, + funannotate_compare, funannotate_predict, funannotate_sort
  • Description: + Funannotate is a genome prediction, annotation, and comparison software package.
  • bio.tool + id: funannotate
  • bio.tool ids: funannotate
  • biii: + nan
  • bio.tool name: funannotate
  • bio.tool description: + funannotate is a pipeline for genome annotation (built specifically for fungi, + but will also work with higher eukaryotes).
  • EDAM operation: + Genome annotation
  • EDAM topic: Genomics
  • Status: + To update
  • Source: https://funannotate.readthedocs.io
  • ToolShed + categories: Genome annotation
  • ToolShed id: nan
  • Date + of first commit of the suite: 2021-08-26
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate
  • Galaxy + wrapper version: 1.8.15
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): Genome + annotation
  • EDAM topic (no superclasses): Genomics
  • Available + on UseGalaxy.org (Main): 3
  • Available on UseGalaxy.org.au: + 5
  • Available on UseGalaxy.eu: 5
  • Available + on UseGalaxy.fr: 5
  • Tools available on UseGalaxy.org (Main): + 3
  • Tools available on UseGalaxy.org.au: 5
  • Tools + available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: + 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 8648
  • No. of tool + users (all time) (usegalaxy.eu): 8648
  • Tool usage (5 years) + (usegalaxy.eu): 1408
  • Tool usage (all time) (usegalaxy.eu): + 1408
  • No. of tool users (5 years) (usegalaxy.org): 32
  • No. + of tool users (all time) (usegalaxy.org): 32
  • Tool usage + (5 years) (usegalaxy.org): 6
  • Tool usage (all time) (usegalaxy.org): + 6
  • No. of tool users (5 years) (usegalaxy.org.au): 6406
  • No. + of tool users (all time) (usegalaxy.org.au): 6406
  • Tool + usage (5 years) (usegalaxy.org.au): 597
  • Tool usage (all + time) (usegalaxy.org.au): 597
  • No. of tool users (5 years) + - all main servers: 15086
  • No. of tool users (all time) + - all main servers: 15086
  • Tool usage (5 years) - all main + servers: 2011
  • Tool usage (all time) - all main servers: + 2011
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: funannotate + - description_md: '
  • Galaxy tool ids: getmlst
  • Description: + Download MLST datasets by species from pubmlst.org
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: nan
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: getmlst
  • Date + of first commit of the suite: 2015-12-03
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: nan
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst
  • Galaxy + wrapper version: 0.1.4.1
  • Conda id: srst2
  • Conda + version: 0.2.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: getmlst + - description_md: '
  • Galaxy tool ids: ggplot2_heatmap, ggplot2_pca, + ggplot2_histogram, ggplot2_point, ggplot2_violin
  • 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.
  • bio.tool + id: ggplot2
  • bio.tool ids: ggplot2
  • biii: + nan
  • bio.tool name: ggplot2
  • bio.tool description: + Plotting system for R, based on the grammar of graphics.
  • EDAM + operation: Visualisation
  • EDAM topic: Data visualisation
  • Status: + To update
  • Source: https://github.com/tidyverse/ggplot2
  • ToolShed + categories: Visualization
  • ToolShed id: nan
  • Date + of first commit of the suite: 2018-04-26
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2
  • Galaxy + wrapper version: 3.4.0
  • Conda id: r-base
  • Conda + version: nan
  • EDAM operation (no superclasses): Visualisation
  • EDAM + topic (no superclasses): Data visualisation
  • Available on + UseGalaxy.org (Main): 5
  • Available on UseGalaxy.org.au: + 5
  • Available on UseGalaxy.eu: 5
  • Available + on UseGalaxy.fr: 5
  • Tools available on UseGalaxy.org (Main): + 5
  • Tools available on UseGalaxy.org.au: 5
  • Tools + available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: + 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: 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.no: + 5
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 24606
  • No. of tool + users (all time) (usegalaxy.eu): 25662
  • Tool usage (5 years) + (usegalaxy.eu): 3463
  • Tool usage (all time) (usegalaxy.eu): + 3630
  • No. of tool users (5 years) (usegalaxy.org): 26805
  • No. + of tool users (all time) (usegalaxy.org): 26808
  • Tool usage + (5 years) (usegalaxy.org): 5143
  • Tool usage (all time) (usegalaxy.org): + 5144
  • No. of tool users (5 years) (usegalaxy.org.au): 8174
  • No. + of tool users (all time) (usegalaxy.org.au): 8237
  • Tool + usage (5 years) (usegalaxy.org.au): 1259
  • Tool usage (all + time) (usegalaxy.org.au): 1279
  • No. of tool users (5 years) + - all main servers: 59585
  • No. of tool users (all time) + - all main servers: 60707
  • Tool usage (5 years) - all main + servers: 9865
  • Tool usage (all time) - all main servers: + 10053
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: ggplot2 + - description_md: '
  • Galaxy tool ids: Fetch Taxonomic Ranks
  • Description: + Fetch taxonomic representation
  • bio.tool id: gi2taxonomy
  • bio.tool + ids: gi2taxonomy
  • biii: nan
  • bio.tool + name: gi2taxonomy
  • 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).
  • EDAM + operation: Database search, ID mapping
  • EDAM topic: + Taxonomy
  • Status: To update
  • Source: + https://bitbucket.org/natefoo/taxonomy
  • ToolShed categories: + Metagenomics
  • ToolShed id: gi2taxonomy
  • Date + of first commit of the suite: 2014-01-27
  • Galaxy wrapper + owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy
  • Galaxy + wrapper version: 1.1.1
  • Conda id: taxonomy
  • Conda + version: 0.10.0
  • EDAM operation (no superclasses): + Database search, ID mapping
  • EDAM topic (no superclasses): + Taxonomy
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 490
  • No. of tool + users (all time) (usegalaxy.eu): 682
  • Tool usage (5 years) + (usegalaxy.eu): 74
  • Tool usage (all time) (usegalaxy.eu): + 109
  • No. of tool users (5 years) (usegalaxy.org): 127
  • No. + of tool users (all time) (usegalaxy.org): 14058
  • Tool usage + (5 years) (usegalaxy.org): 20
  • Tool usage (all time) (usegalaxy.org): + 1798
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 617
  • No. + of tool users (all time) - all main servers: 14740
  • Tool + usage (5 years) - all main servers: 94
  • Tool usage (all + time) - all main servers: 1907
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: gi2taxonomy + - description_md: '
  • 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
  • Description: + Glimmer makes gene predictions.
  • bio.tool id: gemini
  • bio.tool + ids: gemini
  • biii: nan
  • bio.tool name: + GEMINI
  • 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.
  • EDAM + operation: Sequence analysis, Genetic variation analysis
  • EDAM + topic: Sequence analysis
  • Status: To update
  • Source: + https://ccb.jhu.edu/software/glimmer/
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: nan
  • Date of + first commit of the suite: 2017-11-28
  • Galaxy wrapper owner: + bgruening
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer
  • Galaxy + wrapper version: nan
  • Conda id: glimmer
  • Conda + version: 3.02
  • EDAM operation (no superclasses): + Sequence analysis, Genetic variation analysis
  • EDAM topic (no superclasses): + Sequence analysis
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 4
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 4
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 4343
  • No. of tool + users (all time) (usegalaxy.eu): 4343
  • Tool usage (5 years) + (usegalaxy.eu): 407
  • Tool usage (all time) (usegalaxy.eu): + 407
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 4343
  • No. + of tool users (all time) - all main servers: 4343
  • Tool + usage (5 years) - all main servers: 407
  • Tool usage (all + time) - all main servers: 407
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: glimmer + - description_md: '
  • Galaxy tool ids: nan
  • Description: + GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://ccb.jhu.edu/software/glimmerhmm/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: glimmer_hmm
  • Date + of first commit of the suite: 2015-02-28
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm
  • Galaxy + wrapper version: nan
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: glimmer_hmm + - description_md: "
  • Galaxy tool ids: goenrichment, goslimmer
  • Description:\ + \ Performs GO Enrichment analysis.
  • bio.tool id: goenrichment
  • bio.tool\ + \ ids: goenrichment
  • biii: nan
  • bio.tool\ + \ name: GOEnrichment
  • 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.
  • EDAM\ + \ operation: Gene-set enrichment analysis
  • EDAM topic:\ + \ Transcriptomics
  • Status: Up-to-date
  • Source:\ + \ https://github.com/DanFaria/GOEnrichment
  • ToolShed categories:\ + \ Genome annotation
  • ToolShed id: nan
  • Date\ + \ of first commit of the suite: 2018-12-28
  • Galaxy wrapper\ + \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment
  • Galaxy\ + \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment
  • Galaxy\ + \ wrapper version: 2.0.1
  • Conda id: goenrichment
  • Conda\ + \ version: 2.0.1
  • EDAM operation (no superclasses):\ + \ Gene-set enrichment analysis
  • EDAM topic (no superclasses):\ + \ Transcriptomics
  • Available on UseGalaxy.org (Main): 2
  • Available\ + \ on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu:\ + \ 2
  • Available on UseGalaxy.fr: 2
  • Tools available\ + \ on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au:\ + \ 2
  • Tools available on UseGalaxy.eu: 2
  • Tools\ + \ available on UseGalaxy.fr: 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: 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.no: 2
  • Tools\ + \ available on Viral Variant Visualizer (VVV): 0
  • No. of\ + \ tool users (5 years) (usegalaxy.eu): 5800
  • No. of tool\ + \ users (all time) (usegalaxy.eu): 6212
  • Tool usage (5 years)\ + \ (usegalaxy.eu): 826
  • Tool usage (all time) (usegalaxy.eu):\ + \ 871
  • No. of tool users (5 years) (usegalaxy.org): 7756
  • No.\ + \ of tool users (all time) (usegalaxy.org): 7756
  • Tool usage\ + \ (5 years) (usegalaxy.org): 1048
  • Tool usage (all time)\ + \ (usegalaxy.org): 1048
  • No. of tool users (5 years) (usegalaxy.org.au):\ + \ 1149
  • No. of tool users (all time) (usegalaxy.org.au):\ + \ 1149
  • Tool usage (5 years) (usegalaxy.org.au): 215
  • Tool\ + \ usage (all time) (usegalaxy.org.au): 215
  • No. of tool\ + \ users (5 years) - all main servers: 14705
  • No. of tool\ + \ users (all time) - all main servers: 15117
  • Tool usage\ + \ (5 years) - all main servers: 2089
  • Tool usage (all time)\ + \ - all main servers: 2134
  • Reviewed: True
  • To\ + \ keep: True
  • Deprecated: False
" + title_md: goenrichment + - description_md: '
  • Galaxy tool ids: goseq
  • Description: + goseq does selection-unbiased testing for category enrichment amongst differentially + expressed (DE) genes for RNA-seq data
  • bio.tool id: goseq
  • bio.tool + ids: goseq
  • biii: nan
  • bio.tool name: + GOseq
  • bio.tool description: Detect Gene Ontology and/or + other user defined categories which are over/under represented in RNA-seq data.
  • EDAM + operation: Gene functional annotation
  • EDAM topic: + RNA-Seq
  • Status: To update
  • Source: + https://bioconductor.org/packages/release/bioc/html/goseq.html
  • ToolShed + categories: Statistics, RNA, Micro-array Analysis
  • ToolShed + id: goseq
  • Date of first commit of the suite: 2018-09-30
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq
  • Galaxy + wrapper version: 1.50.0
  • Conda id: bioconductor-goseq
  • Conda + version: 1.54.0
  • EDAM operation (no superclasses): + Gene functional annotation
  • EDAM topic (no superclasses): + RNA-Seq
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 20207
  • No. of tool + users (all time) (usegalaxy.eu): 21960
  • Tool usage (5 years) + (usegalaxy.eu): 2807
  • Tool usage (all time) (usegalaxy.eu): + 3139
  • No. of tool users (5 years) (usegalaxy.org): 24488
  • No. + of tool users (all time) (usegalaxy.org): 26198
  • Tool usage + (5 years) (usegalaxy.org): 3066
  • Tool usage (all time) (usegalaxy.org): + 3321
  • No. of tool users (5 years) (usegalaxy.org.au): 4155
  • No. + of tool users (all time) (usegalaxy.org.au): 4155
  • Tool + usage (5 years) (usegalaxy.org.au): 545
  • Tool usage (all + time) (usegalaxy.org.au): 545
  • No. of tool users (5 years) + - all main servers: 48850
  • No. of tool users (all time) + - all main servers: 52313
  • Tool usage (5 years) - all main + servers: 6418
  • Tool usage (all time) - all main servers: + 7005
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: goseq + - description_md: '
  • Galaxy tool ids: graphlan, graphlan_annotate
  • Description: + GraPhlAn is a software tool for producing high-quality circular representations + of taxonomic and phylogenetic trees
  • bio.tool id: graphlan
  • bio.tool + ids: graphlan
  • biii: nan
  • bio.tool name: + GraPhlAn
  • 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.
  • EDAM + operation: Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic + tree editing, Taxonomic classification
  • EDAM topic: Metagenomics, + Phylogenetics, Phylogenomics, Cladistics
  • Status: To update
  • Source: + https://github.com/biobakery/graphlan
  • ToolShed categories: + Metagenomics, Graphics, Phylogenetics
  • ToolShed id: graphlan
  • Date + of first commit of the suite: 2017-03-03
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan
  • Galaxy + wrapper version: nan
  • Conda id: graphlan
  • Conda + version: 1.1.3
  • EDAM operation (no superclasses): + Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, + Taxonomic classification
  • EDAM topic (no superclasses): + Metagenomics, Phylogenetics, Phylogenomics, Cladistics
  • Available + on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: + 2
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: + 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 9816
  • No. of tool + users (all time) (usegalaxy.eu): 10927
  • Tool usage (5 years) + (usegalaxy.eu): 1285
  • Tool usage (all time) (usegalaxy.eu): + 1350
  • No. of tool users (5 years) (usegalaxy.org): 1273
  • No. + of tool users (all time) (usegalaxy.org): 1273
  • Tool usage + (5 years) (usegalaxy.org): 368
  • Tool usage (all time) (usegalaxy.org): + 368
  • No. of tool users (5 years) (usegalaxy.org.au): 1104
  • No. + of tool users (all time) (usegalaxy.org.au): 1104
  • Tool + usage (5 years) (usegalaxy.org.au): 242
  • Tool usage (all + time) (usegalaxy.org.au): 242
  • No. of tool users (5 years) + - all main servers: 12193
  • No. of tool users (all time) + - all main servers: 13304
  • Tool usage (5 years) - all main + servers: 1895
  • Tool usage (all time) - all main servers: + 1960
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: graphlan + - description_md: '
  • Galaxy tool ids: graphmap_align, graphmap_overlap
  • Description: + Mapper for long, error-prone reads.
  • bio.tool id: graphmap
  • bio.tool + ids: graphmap
  • biii: nan
  • bio.tool name: + graphmap
  • 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
  • EDAM operation: + Sequence trimming, EST assembly, Read mapping
  • EDAM topic: + Gene transcripts, RNA-Seq, RNA splicing
  • Status: To update
  • Source: + https://github.com/isovic/graphmap/
  • ToolShed categories: + Assembly
  • ToolShed id: graphmap
  • Date of first + commit of the suite: 2018-09-27
  • Galaxy wrapper owner: + bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/graphmap
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/graphmap
  • Galaxy + wrapper version: 0.5.2
  • Conda id: graphmap
  • Conda + version: 0.6.4
  • EDAM operation (no superclasses): + Sequence trimming, EST assembly, Read mapping
  • EDAM topic (no superclasses): + Gene transcripts, RNA-Seq, RNA splicing
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 2
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 2
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 7012
  • No. of tool users (all time) (usegalaxy.eu): 7344
  • Tool + usage (5 years) (usegalaxy.eu): 323
  • Tool usage (all time) + (usegalaxy.eu): 338
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 7012
  • No. of tool users (all time) - all main + servers: 7344
  • Tool usage (5 years) - all main servers: + 323
  • Tool usage (all time) - all main servers: 338
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: graphmap + - description_md: '
  • Galaxy tool ids: gtdbtk_classify_wf
  • 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.
  • bio.tool + id: GTDB-Tk
  • bio.tool ids: GTDB-Tk
  • biii: + nan
  • bio.tool name: GTDB-Tk
  • 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).
  • EDAM + operation: Genome alignment, Taxonomic classification, Sequence assembly, + Query and retrieval
  • EDAM topic: Metagenomics, Taxonomy, + Phylogenetics, Database management, Proteins
  • Status: Up-to-date
  • Source: + https://github.com/Ecogenomics/GTDBTk
  • ToolShed categories: + Metagenomics
  • ToolShed id: gtdbtk
  • Date of + first commit of the suite: 2022-12-13
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk
  • Galaxy + wrapper version: 2.4.0
  • Conda id: gtdbtk
  • Conda + version: 2.4.0
  • EDAM operation (no superclasses): + Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval
  • EDAM + topic (no superclasses): Metagenomics, Taxonomy, Phylogenetics, Database + management, Proteins
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 476
  • No. of tool users (all time) (usegalaxy.eu): 476
  • Tool + usage (5 years) (usegalaxy.eu): 87
  • Tool usage (all time) + (usegalaxy.eu): 87
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 588
  • No. of tool users (all time) (usegalaxy.org.au): 588
  • Tool + usage (5 years) (usegalaxy.org.au): 74
  • Tool usage (all + time) (usegalaxy.org.au): 74
  • No. of tool users (5 years) + - all main servers: 1064
  • No. of tool users (all time) - + all main servers: 1064
  • Tool usage (5 years) - all main + servers: 161
  • Tool usage (all time) - all main servers: + 161
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: gtdbtk + - description_md: '
  • Galaxy tool ids: gubbins
  • Description: + Gubbins - bacterial recombination detection
  • bio.tool id: + gubbins
  • bio.tool ids: gubbins
  • biii: + nan
  • bio.tool name: Gubbins
  • bio.tool description: + Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant + bacterial whole genome sequences.
  • EDAM operation: Genotyping, + Phylogenetic inference, Ancestral reconstruction
  • EDAM topic: + Phylogeny, Genotype and phenotype, Whole genome sequencing
  • Status: + To update
  • Source: nan
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: gubbins
  • Date + of first commit of the suite: 2017-06-22
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins
  • Galaxy + wrapper version: 3.2.1
  • Conda id: gubbins
  • Conda + version: 3.3.5
  • EDAM operation (no superclasses): + Genotyping, Phylogenetic inference, Ancestral reconstruction
  • EDAM + topic (no superclasses): Phylogeny, Genotype and phenotype, Whole genome + sequencing
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 3690
  • No. of tool + users (all time) (usegalaxy.eu): 3811
  • Tool usage (5 years) + (usegalaxy.eu): 326
  • Tool usage (all time) (usegalaxy.eu): + 336
  • No. of tool users (5 years) (usegalaxy.org): 3323
  • No. + of tool users (all time) (usegalaxy.org): 3323
  • Tool usage + (5 years) (usegalaxy.org): 235
  • Tool usage (all time) (usegalaxy.org): + 235
  • No. of tool users (5 years) (usegalaxy.org.au): 1895
  • No. + of tool users (all time) (usegalaxy.org.au): 2429
  • Tool + usage (5 years) (usegalaxy.org.au): 234
  • Tool usage (all + time) (usegalaxy.org.au): 258
  • No. of tool users (5 years) + - all main servers: 8908
  • No. of tool users (all time) - + all main servers: 9563
  • Tool usage (5 years) - all main + servers: 795
  • Tool usage (all time) - all main servers: + 829
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: gubbins + - description_md: '
  • Galaxy tool ids: hamronize_summarize, hamronize_tool
  • Description: + Convert AMR gene detection tool output to hAMRonization specification format.
  • bio.tool + id: hamronization
  • bio.tool ids: hamronization
  • biii: + nan
  • bio.tool name: hAMRonization
  • bio.tool + description: Parse multiple Antimicrobial Resistance Analysis Reports + into a common data structure
  • EDAM operation: Data handling, + Antimicrobial resistance prediction, Parsing
  • EDAM topic: + Public health and epidemiology, Microbiology, Bioinformatics
  • Status: + Up-to-date
  • Source: https://github.com/pha4ge/hAMRonization
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: hamronization
  • Date + of first commit of the suite: 2021-02-02
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization
  • Galaxy + wrapper version: 1.1.4
  • Conda id: hamronization
  • Conda + version: 1.1.4
  • EDAM operation (no superclasses): + Antimicrobial resistance prediction, Parsing
  • EDAM topic (no superclasses): + Public health and epidemiology, Microbiology, Bioinformatics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: + 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 7303
  • No. of tool + users (all time) (usegalaxy.eu): 7303
  • Tool usage (5 years) + (usegalaxy.eu): 222
  • Tool usage (all time) (usegalaxy.eu): + 222
  • No. of tool users (5 years) (usegalaxy.org): 20
  • No. + of tool users (all time) (usegalaxy.org): 20
  • Tool usage + (5 years) (usegalaxy.org): 2
  • Tool usage (all time) (usegalaxy.org): + 2
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 7323
  • No. + of tool users (all time) - all main servers: 7323
  • Tool + usage (5 years) - all main servers: 224
  • Tool usage (all + time) - all main servers: 224
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: hamronization + - description_md: '
  • Galaxy tool ids: bio_hansel
  • Description: + Heidelberg and Enteritidis SNP Elucidation
  • bio.tool id: + Biohansel
  • bio.tool ids: Biohansel
  • biii: + nan
  • bio.tool name: BioHansel
  • 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.
  • EDAM operation: + Genotyping, SNP detection, Genome assembly
  • EDAM topic: + Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious + disease, Agricultural science
  • Status: Up-to-date
  • Source: + https://github.com/phac-nml/bio_hansel
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: bio_hansel
  • Date + of first commit of the suite: 2017-09-29
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel
  • Galaxy + wrapper version: 2.6.1
  • Conda id: bio_hansel
  • Conda + version: 2.6.1
  • EDAM operation (no superclasses): + Genotyping, SNP detection, Genome assembly
  • EDAM topic (no superclasses): + Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious + disease, Agricultural science
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 349
  • No. of tool users (all time) (usegalaxy.eu): 359
  • Tool + usage (5 years) (usegalaxy.eu): 32
  • Tool usage (all time) + (usegalaxy.eu): 33
  • No. of tool users (5 years) (usegalaxy.org): + 364
  • No. of tool users (all time) (usegalaxy.org): 364
  • Tool + usage (5 years) (usegalaxy.org): 53
  • Tool usage (all time) + (usegalaxy.org): 53
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 713
  • No. of tool users (all time) - all main + servers: 723
  • Tool usage (5 years) - all main servers: + 85
  • Tool usage (all time) - all main servers: 86
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: hansel + - description_md: '
  • Galaxy tool ids: hifiasm_meta
  • Description: + A hifiasm fork for metagenome assembly using Hifi reads.
  • bio.tool + id: hifiasm-meta
  • bio.tool ids: hifiasm-meta
  • biii: + nan
  • bio.tool name: Hifiasm-meta
  • bio.tool + description: Hifiasm_meta - de novo metagenome assembler, based on hifiasm, + a haplotype-resolved de novo assembler for PacBio Hifi reads.
  • EDAM + operation: Sequence assembly
  • EDAM topic: Sequence + assembly, Metagenomics
  • Status: To update
  • Source: + https://github.com/xfengnefx/hifiasm-meta
  • ToolShed categories: + Metagenomics
  • ToolShed id: hifiasm_meta
  • Date + of first commit of the suite: 2023-01-18
  • Galaxy wrapper + owner: galaxy-australia
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta
  • Galaxy + wrapper version: 0.3.1
  • Conda id: hifiasm_meta
  • Conda + version: hamtv0.3.1
  • EDAM operation (no superclasses): + Sequence assembly
  • EDAM topic (no superclasses): Sequence + assembly, Metagenomics
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 156
  • No. of tool users (all time) (usegalaxy.eu): 156
  • Tool + usage (5 years) (usegalaxy.eu): 20
  • Tool usage (all time) + (usegalaxy.eu): 20
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 220
  • No. of tool users (all time) (usegalaxy.org.au): 220
  • Tool + usage (5 years) (usegalaxy.org.au): 11
  • Tool usage (all + time) (usegalaxy.org.au): 11
  • No. of tool users (5 years) + - all main servers: 376
  • No. of tool users (all time) - + all main servers: 376
  • Tool usage (5 years) - all main servers: + 31
  • Tool usage (all time) - all main servers: 31
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: hifiasm_meta + - description_md: '
  • Galaxy tool ids: hivtrace
  • 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.
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + nan
  • ToolShed categories: Sequence Analysis
  • ToolShed + id: hivtrace
  • Date of first commit of the suite: + 2015-12-10
  • Galaxy wrapper owner: nml
  • Galaxy + wrapper source: https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace
  • Galaxy + wrapper version: 1.0.1
  • Conda id: hivtrace
  • Conda + version: 1.5.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: hivtrace + - description_md: '
  • 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
  • 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).
  • bio.tool + id: hmmer3
  • bio.tool ids: hmmer3
  • biii: + nan
  • bio.tool name: HMMER3
  • 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.
  • 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 topic: Sequence analysis, Sequence + sites, features and motifs, Gene and protein families
  • Status: + Up-to-date
  • Source: http://hmmer.org/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: nan
  • Date + of first commit of the suite: 2016-11-14
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3
  • Galaxy + wrapper version: 3.4
  • Conda id: hmmer
  • Conda + version: 3.4
  • 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 (no superclasses): Sequence analysis, Sequence sites, features + and motifs, Gene and protein families
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 12
  • Available + on UseGalaxy.eu: 12
  • Available on UseGalaxy.fr: 12
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 12
  • Tools available on UseGalaxy.eu: + 12
  • Tools available on UseGalaxy.fr: 12
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 12
  • Tools available on Viral + Variant Visualizer (VVV): 0
  • No. of tool users (5 years) + (usegalaxy.eu): 35919
  • No. of tool users (all time) (usegalaxy.eu): + 36952
  • Tool usage (5 years) (usegalaxy.eu): 1283
  • Tool + usage (all time) (usegalaxy.eu): 1321
  • No. of tool users + (5 years) (usegalaxy.org): 0
  • No. of tool users (all time) + (usegalaxy.org): 0
  • Tool usage (5 years) (usegalaxy.org): + 0
  • Tool usage (all time) (usegalaxy.org): 0
  • No. + of tool users (5 years) (usegalaxy.org.au): 3023
  • No. of + tool users (all time) (usegalaxy.org.au): 3023
  • Tool usage + (5 years) (usegalaxy.org.au): 180
  • Tool usage (all time) + (usegalaxy.org.au): 180
  • No. of tool users (5 years) - all + main servers: 38942
  • No. of tool users (all time) - all + main servers: 39975
  • Tool usage (5 years) - all main servers: + 1463
  • Tool usage (all time) - all main servers: 1501
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: hmmer3 + - description_md: "
  • 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
  • Description:\ + \ HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level\ + \ resolution
  • bio.tool id: humann
  • bio.tool\ + \ ids: humann
  • biii: nan
  • bio.tool name:\ + \ humann
  • 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
  • EDAM operation: Species\ + \ frequency estimation, Taxonomic classification, Phylogenetic analysis
  • EDAM\ + \ topic: Metagenomics, Phylogenomics
  • Status: Up-to-date
  • Source:\ + \ http://huttenhower.sph.harvard.edu/humann
  • ToolShed categories:\ + \ Metagenomics
  • ToolShed id: humann
  • Date of\ + \ first commit of the suite: 2021-05-12
  • Galaxy wrapper\ + \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann
  • Galaxy\ + \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann
  • Galaxy\ + \ wrapper version: 3.9
  • Conda id: humann
  • Conda\ + \ version: 3.9
  • EDAM operation (no superclasses):\ + \ Species frequency estimation, Taxonomic classification, Phylogenetic analysis
  • EDAM\ + \ topic (no superclasses): Metagenomics, Phylogenomics
  • Available\ + \ on UseGalaxy.org (Main): 6
  • Available on UseGalaxy.org.au:\ + \ 10
  • Available on UseGalaxy.eu: 10
  • Available\ + \ on UseGalaxy.fr: 10
  • Tools available on UseGalaxy.org\ + \ (Main): 6
  • Tools available on UseGalaxy.org.au:\ + \ 10
  • Tools available on UseGalaxy.eu: 10
  • Tools\ + \ available on UseGalaxy.fr: 10
  • Tools available on APOSTL:\ + \ 0
  • Tools available on ARGs-OAP: 0
  • Tools\ + \ available on CIRM-CFBP: 0
  • Tools available on ChemFlow:\ + \ 0
  • Tools available on Coloc-stats: 0
  • Tools\ + \ available on CropGalaxy: 0
  • Tools available 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.no: 10
  • Tools\ + \ available on Viral Variant Visualizer (VVV): 0
  • No. of\ + \ tool users (5 years) (usegalaxy.eu): 26659
  • No. of tool\ + \ users (all time) (usegalaxy.eu): 26659
  • Tool usage (5\ + \ years) (usegalaxy.eu): 2067
  • Tool usage (all time) (usegalaxy.eu):\ + \ 2067
  • No. of tool users (5 years) (usegalaxy.org): 865
  • No.\ + \ of tool users (all time) (usegalaxy.org): 865
  • Tool usage\ + \ (5 years) (usegalaxy.org): 174
  • Tool usage (all time)\ + \ (usegalaxy.org): 174
  • No. of tool users (5 years) (usegalaxy.org.au):\ + \ 3238
  • No. of tool users (all time) (usegalaxy.org.au):\ + \ 3238
  • Tool usage (5 years) (usegalaxy.org.au): 351
  • Tool\ + \ usage (all time) (usegalaxy.org.au): 351
  • No. of tool\ + \ users (5 years) - all main servers: 30762
  • No. of tool\ + \ users (all time) - all main servers: 30762
  • Tool usage\ + \ (5 years) - all main servers: 2592
  • Tool usage (all time)\ + \ - all main servers: 2592
  • Reviewed: True
  • To\ + \ keep: True
  • Deprecated: False
" + title_md: humann + - description_md: '
  • 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
  • Description: Hypothesis Testing using Phylogenies
  • bio.tool + id: HyPhy
  • bio.tool ids: HyPhy
  • biii: + nan
  • bio.tool name: HyPhy
  • bio.tool description: + Software package for the analysis of genetic sequences using techniques in phylogenetics, + molecular evolution, and machine learning.
  • EDAM operation: + Statistical calculation
  • EDAM topic: Phylogeny, Small molecules, + Molecular interactions, pathways and networks
  • Status: To + update
  • Source: http://www.hyphy.org
  • ToolShed + categories: Phylogenetics
  • ToolShed id: nan
  • Date + of first commit of the suite: 2021-04-19
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy
  • Galaxy + wrapper version: 2.5.47
  • Conda id: hyphy
  • Conda + version: 2.5.62
  • EDAM operation (no superclasses): + Statistical calculation
  • EDAM topic (no superclasses): Phylogeny, + Small molecules, Molecular interactions, pathways and networks
  • Available + on UseGalaxy.org (Main): 17
  • Available on UseGalaxy.org.au: + 2
  • Available on UseGalaxy.eu: 17
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 17
  • Tools available on UseGalaxy.org.au: 2
  • Tools + available on UseGalaxy.eu: 17
  • Tools available on UseGalaxy.fr: + 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 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.no: + 12
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 11429
  • No. of tool + users (all time) (usegalaxy.eu): 11429
  • Tool usage (5 years) + (usegalaxy.eu): 428
  • Tool usage (all time) (usegalaxy.eu): + 428
  • No. of tool users (5 years) (usegalaxy.org): 7751
  • No. + of tool users (all time) (usegalaxy.org): 7751
  • Tool usage + (5 years) (usegalaxy.org): 676
  • Tool usage (all time) (usegalaxy.org): + 676
  • No. of tool users (5 years) (usegalaxy.org.au): 715
  • No. + of tool users (all time) (usegalaxy.org.au): 715
  • Tool usage + (5 years) (usegalaxy.org.au): 58
  • Tool usage (all time) + (usegalaxy.org.au): 58
  • No. of tool users (5 years) - all + main servers: 19895
  • No. of tool users (all time) - all + main servers: 19895
  • Tool usage (5 years) - all main servers: + 1162
  • Tool usage (all time) - all main servers: 1162
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: hyphy + - description_md: '
  • Galaxy tool ids: hypo
  • Description: + Super Fast & Accurate Polisher for Long Read Genome Assemblies
  • bio.tool + id: HyPo
  • bio.tool ids: HyPo
  • biii: + nan
  • bio.tool name: HyPo
  • 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.
  • EDAM + operation: Optimisation and refinement, Genome assembly
  • EDAM + topic: Sequence assembly, Genomics
  • Status: Up-to-date
  • Source: + https://github.com/kensung-lab/hypo
  • ToolShed categories: + Assembly
  • ToolShed id: hypo
  • Date of first + commit of the suite: 2021-11-15
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo
  • Galaxy + wrapper version: 1.0.3
  • Conda id: hypo
  • Conda + version: 1.0.3
  • EDAM operation (no superclasses): + Optimisation and refinement, Genome assembly
  • EDAM topic (no superclasses): + Sequence assembly, Genomics
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 473
  • No. of tool users (all time) (usegalaxy.eu): 473
  • Tool + usage (5 years) (usegalaxy.eu): 93
  • Tool usage (all time) + (usegalaxy.eu): 93
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 473
  • No. of tool users (all time) - all main + servers: 473
  • Tool usage (5 years) - all main servers: + 93
  • Tool usage (all time) - all main servers: 93
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: hypo + - description_md: '
  • Galaxy tool ids: icescreen
  • Description: + ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative + Mobilizable Elements (IMEs) in Bacillota genomes.
  • bio.tool id: + icescreen
  • bio.tool ids: icescreen
  • biii: + nan
  • bio.tool name: ICEscreen
  • bio.tool description: + A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite + structures.
  • EDAM operation: Database search, Protein feature + detection
  • EDAM topic: Mobile genetic elements, Sequence + sites, features and motifs, Genomics, Molecular interactions, pathways and networks, + Structural variation
  • Status: To update
  • Source: + https://icescreen.migale.inrae.fr/
  • ToolShed categories: + Genome annotation
  • ToolShed id: icescreen
  • Date + of first commit of the suite: 2022-01-04
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://forgemia.inra.fr/ices_imes_analysis/icescreen
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen
  • Galaxy + wrapper version: 1.3.1
  • Conda id: icescreen
  • Conda + version: 1.3.2
  • EDAM operation (no superclasses): + Database search, Protein feature detection
  • EDAM topic (no superclasses): + Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular + interactions, pathways and networks, Structural variation
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: icescreen + - description_md: '
  • Galaxy tool ids: idba_hybrid, idba_tran, + idba_ud
  • Description: Wrappers for the idba assembler variants.
  • bio.tool + id: idba
  • bio.tool ids: idba
  • biii: + nan
  • bio.tool name: IDBA
  • 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.
  • EDAM + operation: Sequence assembly
  • EDAM topic: Sequence + assembly
  • Status: To update
  • Source: + https://i.cs.hku.hk/~alse/hkubrg/projects/index.html
  • ToolShed + categories: Assembly
  • ToolShed id: idba
  • Date + of first commit of the suite: 2018-04-26
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud
  • Galaxy + wrapper version: nan
  • Conda id: idba
  • Conda + version: 1.1.3
  • EDAM operation (no superclasses): + Sequence assembly
  • EDAM topic (no superclasses): Sequence + assembly
  • Available on UseGalaxy.org (Main): 3
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 3
  • Available on UseGalaxy.fr: 3
  • Tools available + on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 3
  • Tools + available on UseGalaxy.fr: 3
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools 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.no: + 3
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1200
  • No. of tool + users (all time) (usegalaxy.eu): 1220
  • Tool usage (5 years) + (usegalaxy.eu): 187
  • Tool usage (all time) (usegalaxy.eu): + 195
  • No. of tool users (5 years) (usegalaxy.org): 1588
  • No. + of tool users (all time) (usegalaxy.org): 1588
  • Tool usage + (5 years) (usegalaxy.org): 267
  • Tool usage (all time) (usegalaxy.org): + 267
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 2788
  • No. + of tool users (all time) - all main servers: 2808
  • Tool + usage (5 years) - all main servers: 454
  • Tool usage (all + time) - all main servers: 462
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: idba_ud + - description_md: '
  • Galaxy tool ids: infernal_cmalign, infernal_cmbuild, + infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat
  • Description: + Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.
  • bio.tool id: + infernal
  • bio.tool ids: infernal
  • biii: + nan
  • bio.tool name: Infernal
  • 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.
  • EDAM operation: Nucleic acid feature + detection
  • EDAM topic: Sequence sites, features and motifs, + Structural genomics
  • Status: To update
  • Source: + http://infernal.janelia.org/
  • ToolShed categories: RNA
  • ToolShed + id: infernal
  • Date of first commit of the suite: + 2015-05-07
  • Galaxy wrapper owner: bgruening
  • Galaxy + wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/infernal
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal
  • Galaxy + wrapper version: 1.1.4
  • Conda id: infernal
  • Conda + version: 1.1.5
  • EDAM operation (no superclasses): + Nucleic acid feature detection
  • EDAM topic (no superclasses): + Sequence sites, features and motifs, Structural genomics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 6
  • Available on UseGalaxy.eu: 6
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 6
  • Tools + available on UseGalaxy.eu: 6
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 6
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 59700
  • No. of tool + users (all time) (usegalaxy.eu): 112582
  • Tool usage (5 years) + (usegalaxy.eu): 223
  • Tool usage (all time) (usegalaxy.eu): + 282
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 1157
  • No. + of tool users (all time) (usegalaxy.org.au): 1221
  • Tool + usage (5 years) (usegalaxy.org.au): 34
  • Tool usage (all + time) (usegalaxy.org.au): 35
  • No. of tool users (5 years) + - all main servers: 60857
  • No. of tool users (all time) + - all main servers: 113803
  • Tool usage (5 years) - all main + servers: 257
  • Tool usage (all time) - all main servers: + 317
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: infernal + - description_md: '
  • Galaxy tool ids: instrain_compare, instrain_profile
  • Description: + InStrain is a tool for analysis of co-occurring genome populations from metagenomes
  • bio.tool + id: instrain
  • bio.tool ids: instrain
  • biii: + nan
  • bio.tool name: InStrain
  • 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
  • EDAM operation: SNP detection, + Genome comparison
  • EDAM topic: Mapping, Metagenomics
  • Status: + To update
  • Source: https://instrain.readthedocs.io/en/latest/#
  • ToolShed + categories: Metagenomics
  • ToolShed id: instrain
  • Date + of first commit of the suite: 2021-08-11
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain
  • Galaxy + wrapper version: 1.5.3
  • Conda id: instrain
  • Conda + version: 1.9.0
  • EDAM operation (no superclasses): + SNP detection, Genome comparison
  • EDAM topic (no superclasses): + Mapping, Metagenomics
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 2
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 102
  • No. of tool users (all time) (usegalaxy.eu): 102
  • Tool + usage (5 years) (usegalaxy.eu): 16
  • Tool usage (all time) + (usegalaxy.eu): 16
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 102
  • No. of tool users (all time) - all main + servers: 102
  • Tool usage (5 years) - all main servers: + 16
  • Tool usage (all time) - all main servers: 16
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: instrain + - description_md: '
  • Galaxy tool ids: integron_finder
  • 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"
  • bio.tool + id: integron_finder
  • bio.tool ids: integron_finder
  • biii: + nan
  • bio.tool name: Integron Finder
  • bio.tool + description: A tool to detect Integron in DNA sequences.
  • EDAM + operation: Nucleic acid feature detection, Sequence motif recognition, + Protein feature detection, Genome annotation
  • EDAM topic: + Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis
  • Status: + Up-to-date
  • Source: https://github.com/gem-pasteur/Integron_Finder
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: integronfinder
  • Date + of first commit of the suite: 2022-09-22
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder
  • Galaxy + wrapper version: 2.0.5
  • Conda id: integron_finder
  • Conda + version: 2.0.5
  • EDAM operation (no superclasses): + Nucleic acid feature detection, Sequence motif recognition, Protein feature + detection, Genome annotation
  • EDAM topic (no superclasses): + Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 55149
  • No. of tool + users (all time) (usegalaxy.eu): 55149
  • Tool usage (5 years) + (usegalaxy.eu): 161
  • Tool usage (all time) (usegalaxy.eu): + 161
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 6085
  • No. + of tool users (all time) (usegalaxy.org.au): 6085
  • Tool + usage (5 years) (usegalaxy.org.au): 73
  • Tool usage (all + time) (usegalaxy.org.au): 73
  • No. of tool users (5 years) + - all main servers: 61234
  • No. of tool users (all time) + - all main servers: 61234
  • Tool usage (5 years) - all main + servers: 234
  • Tool usage (all time) - all main servers: + 234
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: integron_finder + - description_md: '
  • Galaxy tool ids: interproscan
  • Description: + Interproscan queries the interpro database and provides annotations.
  • bio.tool + id: interproscan_ebi
  • bio.tool ids: interproscan_ebi
  • biii: + nan
  • bio.tool name: InterProScan (EBI)
  • bio.tool + description: Scan sequences against the InterPro protein signature databases.
  • EDAM + operation: Sequence motif recognition, Protein feature detection
  • EDAM + topic: Gene and protein families, Sequence analysis
  • Status: + To update
  • Source: http://www.ebi.ac.uk/Tools/pfa/iprscan5/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: interproscan
  • Date + of first commit of the suite: 2021-11-15
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan
  • Galaxy + wrapper version: 5.59-91.0
  • Conda id: interproscan
  • Conda + version: 5.59_91.0
  • EDAM operation (no superclasses): + Sequence motif recognition, Protein feature detection
  • EDAM topic + (no superclasses): Gene and protein families, Sequence analysis
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 34689
  • No. of tool + users (all time) (usegalaxy.eu): 55189
  • Tool usage (5 years) + (usegalaxy.eu): 1634
  • Tool usage (all time) (usegalaxy.eu): + 1713
  • No. of tool users (5 years) (usegalaxy.org): 65
  • No. + of tool users (all time) (usegalaxy.org): 65
  • Tool usage + (5 years) (usegalaxy.org): 15
  • Tool usage (all time) (usegalaxy.org): + 15
  • No. of tool users (5 years) (usegalaxy.org.au): 10897
  • No. + of tool users (all time) (usegalaxy.org.au): 10897
  • Tool + usage (5 years) (usegalaxy.org.au): 607
  • Tool usage (all + time) (usegalaxy.org.au): 607
  • No. of tool users (5 years) + - all main servers: 45651
  • No. of tool users (all time) + - all main servers: 66151
  • Tool usage (5 years) - all main + servers: 2256
  • Tool usage (all time) - all main servers: + 2335
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: interproscan + - description_md: '
  • Galaxy tool ids: nan
  • Description: + Interproscan queries the interpro database and provides annotations.
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: http://www.ebi.ac.uk/Tools/pfa/iprscan5/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: iprscan5
  • Date + of first commit of the suite: 2015-02-28
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5
  • Galaxy + wrapper version: nan
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: iprscan5 + - description_md: '
  • Galaxy tool ids: iqtree
  • Description: + Efficient phylogenomic software by maximum likelihood
  • bio.tool + id: iqtree
  • bio.tool ids: iqtree
  • biii: + nan
  • bio.tool name: iqtree
  • 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
  • EDAM operation: Phylogenetic + analysis, Sequence analysis
  • EDAM topic: Phylogenetics
  • Status: + Up-to-date
  • Source: http://www.iqtree.org/
  • ToolShed + categories: Phylogenetics
  • ToolShed id: iqtree
  • Date + of first commit of the suite: 2017-11-15
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree
  • Galaxy + wrapper version: 2.3.6
  • Conda id: iqtree
  • Conda + version: 2.3.6
  • EDAM operation (no superclasses): + Phylogenetic analysis, Sequence analysis
  • EDAM topic (no superclasses): + Phylogenetics
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 28279
  • No. of tool + users (all time) (usegalaxy.eu): 28481
  • Tool usage (5 years) + (usegalaxy.eu): 1623
  • Tool usage (all time) (usegalaxy.eu): + 1646
  • No. of tool users (5 years) (usegalaxy.org): 24662
  • No. + of tool users (all time) (usegalaxy.org): 24662
  • Tool usage + (5 years) (usegalaxy.org): 2093
  • Tool usage (all time) (usegalaxy.org): + 2093
  • No. of tool users (5 years) (usegalaxy.org.au): 9780
  • No. + of tool users (all time) (usegalaxy.org.au): 10086
  • Tool + usage (5 years) (usegalaxy.org.au): 979
  • Tool usage (all + time) (usegalaxy.org.au): 992
  • No. of tool users (5 years) + - all main servers: 62721
  • No. of tool users (all time) + - all main servers: 63229
  • Tool usage (5 years) - all main + servers: 4695
  • Tool usage (all time) - all main servers: + 4731
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: iqtree + - description_md: '
  • Galaxy tool ids: isescan
  • 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."
  • bio.tool id: ISEScan
  • bio.tool + ids: ISEScan
  • biii: nan
  • bio.tool name: + ISEScan
  • bio.tool description: Automated identification + of insertion sequence elements in prokaryotic genomes.
  • EDAM operation: + Structural variation detection
  • EDAM topic: Genomics, DNA + structural variation, Sequence analysis, Genetic variation
  • Status: + To update
  • Source: https://github.com/xiezhq/ISEScan
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: ISEScan
  • Date + of first commit of the suite: 2022-09-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan
  • Galaxy + wrapper version: 1.7.2.3
  • Conda id: isescan
  • Conda + version: 1.7.2.1
  • EDAM operation (no superclasses): + Structural variation detection
  • EDAM topic (no superclasses): + Genomics, Sequence analysis, Genetic variation
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 59386
  • No. of tool users (all time) (usegalaxy.eu): 59386
  • Tool + usage (5 years) (usegalaxy.eu): 151
  • Tool usage (all time) + (usegalaxy.eu): 151
  • No. of tool users (5 years) (usegalaxy.org): + 56
  • No. of tool users (all time) (usegalaxy.org): 56
  • Tool + usage (5 years) (usegalaxy.org): 1
  • Tool usage (all time) + (usegalaxy.org): 1
  • No. of tool users (5 years) (usegalaxy.org.au): + 4741
  • No. of tool users (all time) (usegalaxy.org.au): 4741
  • Tool + usage (5 years) (usegalaxy.org.au): 59
  • Tool usage (all + time) (usegalaxy.org.au): 59
  • No. of tool users (5 years) + - all main servers: 64183
  • No. of tool users (all time) + - all main servers: 64183
  • Tool usage (5 years) - all main + servers: 211
  • Tool usage (all time) - all main servers: + 211
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: isescan + - description_md: '
  • Galaxy tool ids: itsx
  • Description: + ITSx is an open source software utility to extract the highly variable ITS1 + and ITS2 subregions from ITS sequences.
  • bio.tool id: ITSx
  • bio.tool + ids: ITSx
  • biii: nan
  • bio.tool name: + ITSx
  • 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.
  • EDAM + operation: Sequence feature detection
  • EDAM topic: + Functional, regulatory and non-coding RNA, Microbiology
  • Status: + Up-to-date
  • Source: https://microbiology.se/software/itsx/
  • ToolShed + categories: Metagenomics
  • ToolShed id: itsx
  • Date + of first commit of the suite: 2022-05-02
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/itsx
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/itsx
  • Galaxy + wrapper version: 1.1.3
  • Conda id: itsx
  • Conda + version: 1.1.3
  • EDAM operation (no superclasses): + Sequence feature detection
  • EDAM topic (no superclasses): + Functional, regulatory and non-coding RNA, Microbiology
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1426
  • No. of tool + users (all time) (usegalaxy.eu): 1426
  • Tool usage (5 years) + (usegalaxy.eu): 71
  • Tool usage (all time) (usegalaxy.eu): + 71
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1426
  • No. + of tool users (all time) - all main servers: 1426
  • Tool + usage (5 years) - all main servers: 71
  • Tool usage (all + time) - all main servers: 71
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: itsx + - description_md: '
  • Galaxy tool ids: ivar_consensus, ivar_filtervariants, + ivar_removereads, ivar_trim, ivar_variants
  • Description: + iVar is a computational package that contains functions broadly useful for viral + amplicon-based sequencing
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: + https://github.com/andersen-lab/ivar
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: ivar
  • Date + of first commit of the suite: 2020-06-05
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar
  • Galaxy + wrapper version: 1.4.3
  • Conda id: ivar
  • Conda + version: 1.4.3
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 5
  • Available on UseGalaxy.org.au: + 5
  • Available on UseGalaxy.eu: 5
  • Available + on UseGalaxy.fr: 5
  • Tools available on UseGalaxy.org (Main): + 5
  • Tools available on UseGalaxy.org.au: 5
  • Tools + available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: + 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: + 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.no: + 5
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1252220
  • No. of + tool users (all time) (usegalaxy.eu): 1252220
  • Tool usage + (5 years) (usegalaxy.eu): 2366
  • Tool usage (all time) (usegalaxy.eu): + 2366
  • No. of tool users (5 years) (usegalaxy.org): 126027
  • No. + of tool users (all time) (usegalaxy.org): 126027
  • Tool usage + (5 years) (usegalaxy.org): 2496
  • Tool usage (all time) (usegalaxy.org): + 2496
  • No. of tool users (5 years) (usegalaxy.org.au): 41901
  • No. + of tool users (all time) (usegalaxy.org.au): 41901
  • Tool + usage (5 years) (usegalaxy.org.au): 993
  • Tool usage (all + time) (usegalaxy.org.au): 993
  • No. of tool users (5 years) + - all main servers: 1420148
  • No. of tool users (all time) + - all main servers: 1420148
  • Tool usage (5 years) - all + main servers: 5855
  • Tool usage (all time) - all main servers: + 5855
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: ivar + - description_md: '
  • Galaxy tool ids: jbrowse_to_standalone, + jbrowse
  • Description: JBrowse Genome Browser integrated + as a Galaxy Tool
  • bio.tool id: jbrowse
  • bio.tool + ids: jbrowse
  • biii: nan
  • bio.tool name: + JBrowse
  • 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.
  • EDAM + operation: Genome visualisation
  • EDAM topic: Genomics
  • Status: + Up-to-date
  • Source: https://jbrowse.org
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: jbrowse
  • Date + of first commit of the suite: 2019-08-29
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse
  • Galaxy + wrapper version: 1.16.11
  • Conda id: jbrowse
  • Conda + version: 1.16.11
  • EDAM operation (no superclasses): + Genome visualisation
  • EDAM topic (no superclasses): Genomics
  • Available + on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: + 2
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 21153
  • No. of tool + users (all time) (usegalaxy.eu): 22174
  • Tool usage (5 years) + (usegalaxy.eu): 5514
  • Tool usage (all time) (usegalaxy.eu): + 5779
  • No. of tool users (5 years) (usegalaxy.org): 17428
  • No. + of tool users (all time) (usegalaxy.org): 17428
  • Tool usage + (5 years) (usegalaxy.org): 6458
  • Tool usage (all time) (usegalaxy.org): + 6458
  • No. of tool users (5 years) (usegalaxy.org.au): 15673
  • No. + of tool users (all time) (usegalaxy.org.au): 17267
  • Tool + usage (5 years) (usegalaxy.org.au): 3248
  • Tool usage (all + time) (usegalaxy.org.au): 3786
  • No. of tool users (5 years) + - all main servers: 54254
  • No. of tool users (all time) + - all main servers: 56869
  • Tool usage (5 years) - all main + servers: 15220
  • Tool usage (all time) - all main servers: + 16023
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: jbrowse + - description_md: '
  • Galaxy tool ids: jellyfish
  • Description: + Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA
  • bio.tool + id: Jellyfish
  • bio.tool ids: Jellyfish
  • biii: + nan
  • bio.tool name: Jellyfish
  • bio.tool description: + A command-line algorithm for counting k-mers in DNA sequence.
  • EDAM + operation: k-mer counting
  • EDAM topic: Sequence analysis, + Genomics
  • Status: To update
  • Source: + https://github.com/gmarcais/Jellyfish
  • ToolShed categories: + Assembly
  • ToolShed id: jellyfish
  • Date of first + commit of the suite: 2021-04-07
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish
  • Galaxy + wrapper version: nan
  • Conda id: kmer-jellyfish
  • Conda + version: 2.3.1
  • EDAM operation (no superclasses): + k-mer counting
  • EDAM topic (no superclasses): Sequence analysis, + Genomics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1825
  • No. of tool + users (all time) (usegalaxy.eu): 1825
  • Tool usage (5 years) + (usegalaxy.eu): 237
  • Tool usage (all time) (usegalaxy.eu): + 237
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 971
  • No. + of tool users (all time) (usegalaxy.org.au): 971
  • Tool usage + (5 years) (usegalaxy.org.au): 56
  • Tool usage (all time) + (usegalaxy.org.au): 56
  • No. of tool users (5 years) - all + main servers: 2796
  • No. of tool users (all time) - all main + servers: 2796
  • Tool usage (5 years) - all main servers: + 293
  • Tool usage (all time) - all main servers: 293
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: jellyfish + - description_md: '
  • Galaxy tool ids: kat_@EXECUTABLE@
  • Description: + Filtering kmers or reads from a database of kmers hashes
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: nan
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: kat_filter
  • Date + of first commit of the suite: 2017-03-13
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: nan
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter
  • Galaxy + wrapper version: 2.3
  • Conda id: kat
  • Conda + version: 2.4.2
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: kat_filter + - description_md: '
  • Galaxy tool ids: kc-align
  • Description: + Kc-Align custom tool
  • bio.tool id: kc-align
  • bio.tool + ids: kc-align
  • biii: nan
  • bio.tool name: + kc-align
  • bio.tool description: A fast and accurate tool + for performing codon-aware multiple sequence alignments
  • EDAM operation: + Multiple sequence alignment
  • EDAM topic: Mapping
  • Status: + Up-to-date
  • Source: https://github.com/davebx/kc-align
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: kc_align
  • Date + of first commit of the suite: 2020-02-20
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align
  • Galaxy + wrapper version: 1.0.2
  • Conda id: kcalign
  • Conda + version: 1.0.2
  • EDAM operation (no superclasses): + Multiple sequence alignment
  • EDAM topic (no superclasses): + Mapping
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 379
  • No. of tool + users (all time) (usegalaxy.eu): 379
  • Tool usage (5 years) + (usegalaxy.eu): 53
  • Tool usage (all time) (usegalaxy.eu): + 53
  • No. of tool users (5 years) (usegalaxy.org): 8259
  • No. + of tool users (all time) (usegalaxy.org): 8259
  • Tool usage + (5 years) (usegalaxy.org): 271
  • Tool usage (all time) (usegalaxy.org): + 271
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 8638
  • No. + of tool users (all time) - all main servers: 8638
  • Tool + usage (5 years) - all main servers: 324
  • Tool usage (all + time) - all main servers: 324
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: kc-align + - description_md: '
  • 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
  • Description: + In-memory nucleotide sequence k-mer counting, filtering, graph traversal and + more
  • bio.tool id: khmer
  • bio.tool ids: + khmer
  • biii: nan
  • bio.tool name: khmer
  • 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.
  • EDAM operation: + Standardisation and normalisation, De-novo assembly
  • EDAM topic: + Sequence assembly
  • Status: Up-to-date
  • Source: + https://khmer.readthedocs.org/
  • ToolShed categories: Assembly, + Next Gen Mappers
  • ToolShed id: khmer
  • Date + of first commit of the suite: 2015-11-08
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer
  • Galaxy + wrapper version: 3.0.0a3
  • Conda id: khmer
  • Conda + version: 3.0.0a3
  • EDAM operation (no superclasses): + Standardisation and normalisation, De-novo assembly
  • EDAM topic + (no superclasses): Sequence assembly
  • Available on UseGalaxy.org + (Main): 8
  • Available on UseGalaxy.org.au: 8
  • Available + on UseGalaxy.eu: 8
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 8
  • Tools available on + UseGalaxy.org.au: 8
  • Tools available on UseGalaxy.eu: + 8
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available 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.no: 8
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1995
  • No. of tool users (all time) (usegalaxy.eu): 2091
  • Tool + usage (5 years) (usegalaxy.eu): 174
  • Tool usage (all time) + (usegalaxy.eu): 193
  • No. of tool users (5 years) (usegalaxy.org): + 1430
  • No. of tool users (all time) (usegalaxy.org): 1430
  • Tool + usage (5 years) (usegalaxy.org): 389
  • Tool usage (all time) + (usegalaxy.org): 389
  • No. of tool users (5 years) (usegalaxy.org.au): + 1580
  • No. of tool users (all time) (usegalaxy.org.au): 1580
  • Tool + usage (5 years) (usegalaxy.org.au): 56
  • Tool usage (all + time) (usegalaxy.org.au): 56
  • No. of tool users (5 years) + - all main servers: 5005
  • No. of tool users (all time) - + all main servers: 5101
  • Tool usage (5 years) - all main + servers: 619
  • Tool usage (all time) - all main servers: + 638
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: khmer + - description_md: '
  • Galaxy tool ids: kleborate
  • Description: + Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae + species complex (KpSC)
  • bio.tool id: kleborate
  • bio.tool + ids: kleborate
  • biii: nan
  • bio.tool + name: Kleborate
  • 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).
  • EDAM + operation: Multilocus sequence typing, Genome assembly, Virulence prediction
  • EDAM + topic: Public health and epidemiology, Metagenomics, Population genomics, + Sequence assembly, Whole genome sequencing
  • Status: To update
  • Source: + https://github.com/katholt/Kleborate/wiki
  • ToolShed categories: + Metagenomics
  • ToolShed id: kleborate
  • Date + of first commit of the suite: 2022-09-09
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/katholt/Kleborate
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate
  • Galaxy + wrapper version: 2.3.2
  • Conda id: kleborate
  • Conda + version: 3.1.0
  • EDAM operation (no superclasses): + Multilocus sequence typing, Genome assembly, Virulence prediction
  • EDAM + topic (no superclasses): Public health and epidemiology, Metagenomics, + Population genomics, Sequence assembly, Whole genome sequencing
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 503
  • No. of tool + users (all time) (usegalaxy.eu): 503
  • Tool usage (5 years) + (usegalaxy.eu): 58
  • Tool usage (all time) (usegalaxy.eu): + 58
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 503
  • No. + of tool users (all time) - all main servers: 503
  • Tool usage + (5 years) - all main servers: 58
  • Tool usage (all time) + - all main servers: 58
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: kleborate + - description_md: '
  • Galaxy tool ids: kofamscan
  • Description: + Gene function annotation tool based on KEGG Orthology and hidden Markov model
  • bio.tool + id: kofamscan
  • bio.tool ids: kofamscan
  • biii: + nan
  • bio.tool name: kofamscan
  • 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.
  • EDAM operation: + Sequence analysis, Gene functional annotation
  • EDAM topic: + Genomics
  • Status: Up-to-date
  • Source: + https://github.com/takaram/kofam_scan
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: kofamscan
  • Date + of first commit of the suite: 2020-11-12
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan
  • Galaxy + wrapper version: 1.3.0
  • Conda id: kofamscan
  • Conda + version: 1.3.0
  • EDAM operation (no superclasses): + Sequence analysis, Gene functional annotation
  • EDAM topic (no superclasses): + Genomics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1342
  • No. of tool + users (all time) (usegalaxy.eu): 1342
  • Tool usage (5 years) + (usegalaxy.eu): 63
  • Tool usage (all time) (usegalaxy.eu): + 63
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1342
  • No. + of tool users (all time) - all main servers: 1342
  • Tool + usage (5 years) - all main servers: 63
  • Tool usage (all + time) - all main servers: 63
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: kofamscan + - description_md: '
  • Galaxy tool ids: kraken-filter, kraken-mpa-report, + kraken-report, kraken-translate, kraken
  • 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.
  • bio.tool id: kraken
  • bio.tool ids: + kraken
  • biii: nan
  • bio.tool name: Kraken
  • 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.
  • EDAM operation: Taxonomic + classification
  • EDAM topic: Taxonomy, Metagenomics
  • Status: + To update
  • Source: http://ccb.jhu.edu/software/kraken/
  • ToolShed + categories: Metagenomics
  • ToolShed id: kraken
  • Date + of first commit of the suite: 2017-01-24
  • Galaxy wrapper + owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken
  • Galaxy + wrapper version: nan
  • Conda id: kraken
  • Conda + version: 1.1.1
  • EDAM operation (no superclasses): + Taxonomic classification
  • EDAM topic (no superclasses): + Taxonomy, Metagenomics
  • Available on UseGalaxy.org (Main): + 5
  • Available on UseGalaxy.org.au: 5
  • Available + on UseGalaxy.eu: 5
  • Available on UseGalaxy.fr: 5
  • Tools + available on UseGalaxy.org (Main): 5
  • Tools available on + UseGalaxy.org.au: 5
  • Tools available on UseGalaxy.eu: + 5
  • Tools available on UseGalaxy.fr: 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: 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.no: 5
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 48136
  • No. of tool users (all time) (usegalaxy.eu): 48164
  • Tool + usage (5 years) (usegalaxy.eu): 2754
  • Tool usage (all time) + (usegalaxy.eu): 2760
  • No. of tool users (5 years) (usegalaxy.org): + 59952
  • No. of tool users (all time) (usegalaxy.org): 130398
  • Tool + usage (5 years) (usegalaxy.org): 5869
  • Tool usage (all time) + (usegalaxy.org): 8654
  • No. of tool users (5 years) (usegalaxy.org.au): + 29008
  • No. of tool users (all time) (usegalaxy.org.au): + 31148
  • Tool usage (5 years) (usegalaxy.org.au): 1936
  • Tool + usage (all time) (usegalaxy.org.au): 2200
  • No. of tool users + (5 years) - all main servers: 137096
  • No. of tool users + (all time) - all main servers: 209710
  • Tool usage (5 years) + - all main servers: 10559
  • Tool usage (all time) - all main + servers: 13614
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: kraken + - description_md: '
  • Galaxy tool ids: kraken2
  • Description: + Kraken2 for taxonomic designation.
  • bio.tool id: kraken2
  • bio.tool + ids: kraken2
  • biii: nan
  • bio.tool name: + kraken2
  • 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.
  • EDAM + operation: Taxonomic classification
  • EDAM topic: + Taxonomy, Metagenomics
  • Status: Up-to-date
  • Source: + http://ccb.jhu.edu/software/kraken/
  • ToolShed categories: + Metagenomics
  • ToolShed id: kraken2
  • Date of + first commit of the suite: 2019-03-06
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2
  • Galaxy + wrapper version: 2.1.3
  • Conda id: kraken2
  • Conda + version: 2.1.3
  • EDAM operation (no superclasses): + Taxonomic classification
  • EDAM topic (no superclasses): + Taxonomy, Metagenomics
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 271367
  • No. of tool users (all time) (usegalaxy.eu): 271786
  • Tool + usage (5 years) (usegalaxy.eu): 6384
  • Tool usage (all time) + (usegalaxy.eu): 6409
  • No. of tool users (5 years) (usegalaxy.org): + 101752
  • No. of tool users (all time) (usegalaxy.org): 101752
  • Tool + usage (5 years) (usegalaxy.org): 4662
  • Tool usage (all time) + (usegalaxy.org): 4662
  • No. of tool users (5 years) (usegalaxy.org.au): + 53562
  • No. of tool users (all time) (usegalaxy.org.au): + 53562
  • Tool usage (5 years) (usegalaxy.org.au): 1663
  • Tool + usage (all time) (usegalaxy.org.au): 1663
  • No. of tool users + (5 years) - all main servers: 426681
  • No. of tool users + (all time) - all main servers: 427100
  • Tool usage (5 years) + - all main servers: 12709
  • Tool usage (all time) - all main + servers: 12734
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: kraken2 + - description_md: '
  • Galaxy tool ids: Kraken2Tax
  • Description: + Convert Kraken output to Galaxy taxonomy data.
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: https://bitbucket.org/natefoo/taxonomy
  • ToolShed + categories: Metagenomics
  • ToolShed id: kraken2tax
  • Date + of first commit of the suite: 2015-08-05
  • Galaxy wrapper + owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax
  • Galaxy + wrapper version: 1.2+galaxy0
  • Conda id: gawk
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 23008
  • No. of tool users (all time) (usegalaxy.eu): 23014
  • Tool + usage (5 years) (usegalaxy.eu): 1060
  • Tool usage (all time) + (usegalaxy.eu): 1061
  • No. of tool users (5 years) (usegalaxy.org): + 16194
  • No. of tool users (all time) (usegalaxy.org): 24490
  • Tool + usage (5 years) (usegalaxy.org): 1719
  • Tool usage (all time) + (usegalaxy.org): 2168
  • No. of tool users (5 years) (usegalaxy.org.au): + 14898
  • No. of tool users (all time) (usegalaxy.org.au): + 14898
  • Tool usage (5 years) (usegalaxy.org.au): 436
  • Tool + usage (all time) (usegalaxy.org.au): 436
  • No. of tool users + (5 years) - all main servers: 54100
  • No. of tool users (all + time) - all main servers: 62402
  • Tool usage (5 years) - + all main servers: 3215
  • Tool usage (all time) - all main + servers: 3665
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: kraken2tax + - description_md: '
  • Galaxy tool ids: kraken_biom
  • Description: + Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: Up-to-date
  • Source: https://github.com/smdabdoub/kraken-biom
  • ToolShed + categories: Metagenomics
  • ToolShed id: kraken_biom
  • Date + of first commit of the suite: 2022-09-03
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/smdabdoub/kraken-biom
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom
  • Galaxy + wrapper version: 1.2.0
  • Conda id: kraken-biom
  • Conda + version: 1.2.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 3185
  • No. of tool + users (all time) (usegalaxy.eu): 3185
  • Tool usage (5 years) + (usegalaxy.eu): 495
  • Tool usage (all time) (usegalaxy.eu): + 495
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 385
  • No. + of tool users (all time) (usegalaxy.org.au): 385
  • Tool usage + (5 years) (usegalaxy.org.au): 48
  • Tool usage (all time) + (usegalaxy.org.au): 48
  • No. of tool users (5 years) - all + main servers: 3570
  • No. of tool users (all time) - all main + servers: 3570
  • Tool usage (5 years) - all main servers: + 543
  • Tool usage (all time) - all main servers: 543
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: kraken_biom + - description_md: '
  • Galaxy tool ids: kraken_taxonomy_report
  • Description: + Kraken taxonomy report
  • bio.tool id: Kraken-Taxonomy-Report
  • bio.tool + ids: Kraken-Taxonomy-Report
  • biii: nan
  • bio.tool + name: Kraken-Taxonomy-Report
  • bio.tool description: + view report of classification for multiple samples
  • EDAM operation: + Visualisation, Classification
  • EDAM topic: Metagenomics, + Taxonomy
  • Status: To update
  • Source: + https://github.com/blankenberg/Kraken-Taxonomy-Report
  • ToolShed + categories: Metagenomics
  • ToolShed id: kraken_taxonomy_report
  • Date + of first commit of the suite: 2016-06-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report
  • Galaxy + wrapper version: 0.0.3
  • Conda id: biopython
  • Conda + version: 1.70
  • EDAM operation (no superclasses): + Visualisation, Classification
  • EDAM topic (no superclasses): + Metagenomics, Taxonomy
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 3981
  • No. of tool users (all time) (usegalaxy.eu): 3986
  • Tool + usage (5 years) (usegalaxy.eu): 769
  • Tool usage (all time) + (usegalaxy.eu): 771
  • No. of tool users (5 years) (usegalaxy.org): + 4087
  • No. of tool users (all time) (usegalaxy.org): 5610
  • Tool + usage (5 years) (usegalaxy.org): 991
  • Tool usage (all time) + (usegalaxy.org): 1284
  • No. of tool users (5 years) (usegalaxy.org.au): + 88
  • No. of tool users (all time) (usegalaxy.org.au): 88
  • Tool + usage (5 years) (usegalaxy.org.au): 41
  • Tool usage (all + time) (usegalaxy.org.au): 41
  • No. of tool users (5 years) + - all main servers: 8156
  • No. of tool users (all time) - + all main servers: 9684
  • Tool usage (5 years) - all main + servers: 1801
  • Tool usage (all time) - all main servers: + 2096
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: kraken_taxonomy_report + - description_md: '
  • Galaxy tool ids: krakentools_alpha_diversity, + krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, + krakentools_kreport2krona, krakentools_kreport2mpa
  • Description: + KrakenTools is a suite of scripts to be used alongside the Kraken
  • bio.tool + id: krakentools
  • bio.tool ids: krakentools
  • biii: + nan
  • bio.tool name: KrakenTools
  • bio.tool description: + KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq + output files
  • EDAM operation: Visualisation, Aggregation
  • EDAM + topic: Taxonomy, Metagenomics
  • Status: Up-to-date
  • Source: + https://github.com/jenniferlu717/KrakenTools
  • ToolShed categories: + Metagenomics
  • ToolShed id: krakentools
  • Date + of first commit of the suite: 2023-01-13
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools
  • Galaxy + wrapper version: 1.2
  • Conda id: krakentools
  • Conda + version: 1.2
  • EDAM operation (no superclasses): Visualisation, + Aggregation
  • EDAM topic (no superclasses): Taxonomy, Metagenomics
  • Available + on UseGalaxy.org (Main): 6
  • Available on UseGalaxy.org.au: + 6
  • Available on UseGalaxy.eu: 6
  • Available + on UseGalaxy.fr: 6
  • Tools available on UseGalaxy.org (Main): + 6
  • Tools available on UseGalaxy.org.au: 6
  • Tools + available on UseGalaxy.eu: 6
  • Tools available on UseGalaxy.fr: + 6
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 48516
  • No. of tool + users (all time) (usegalaxy.eu): 48516
  • Tool usage (5 years) + (usegalaxy.eu): 2373
  • Tool usage (all time) (usegalaxy.eu): + 2373
  • No. of tool users (5 years) (usegalaxy.org): 8787
  • No. + of tool users (all time) (usegalaxy.org): 8787
  • Tool usage + (5 years) (usegalaxy.org): 943
  • Tool usage (all time) (usegalaxy.org): + 943
  • No. of tool users (5 years) (usegalaxy.org.au): 4369
  • No. + of tool users (all time) (usegalaxy.org.au): 4369
  • Tool + usage (5 years) (usegalaxy.org.au): 393
  • Tool usage (all + time) (usegalaxy.org.au): 393
  • No. of tool users (5 years) + - all main servers: 61672
  • No. of tool users (all time) + - all main servers: 61672
  • Tool usage (5 years) - all main + servers: 3709
  • Tool usage (all time) - all main servers: + 3709
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: krakentools + - description_md: '
  • Galaxy tool ids: krocus
  • Description: + Predict MLST directly from uncorrected long reads
  • bio.tool id: + krocus
  • bio.tool ids: krocus
  • biii: + nan
  • bio.tool name: krocus
  • bio.tool description: + Predict MLST directly from uncorrected long reads
  • EDAM operation: + Multilocus sequence typing, k-mer counting
  • EDAM topic: + Public health and epidemiology
  • Status: To update
  • Source: + https://github.com/quadram-institute-bioscience/krocus
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: krocus
  • Date + of first commit of the suite: 2019-09-03
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus
  • Galaxy + wrapper version: 1.0.1
  • Conda id: krocus
  • Conda + version: 1.0.3
  • EDAM operation (no superclasses): + Multilocus sequence typing, k-mer counting
  • EDAM topic (no superclasses): + Public health and epidemiology
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: krocus + - description_md: '
  • Galaxy tool ids: lca1
  • Description: + Find lowest diagnostic rank
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://bitbucket.org/natefoo/taxonomy
  • ToolShed categories: + Metagenomics
  • ToolShed id: lca_wrapper
  • Date + of first commit of the suite: 2014-01-27
  • Galaxy wrapper + owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper
  • Galaxy + wrapper version: 1.0.1
  • Conda id: taxonomy
  • Conda + version: 0.10.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 89
  • No. of tool + users (all time) (usegalaxy.eu): 137
  • Tool usage (5 years) + (usegalaxy.eu): 4
  • Tool usage (all time) (usegalaxy.eu): + 20
  • No. of tool users (5 years) (usegalaxy.org): 118
  • No. + of tool users (all time) (usegalaxy.org): 6136
  • Tool usage + (5 years) (usegalaxy.org): 15
  • Tool usage (all time) (usegalaxy.org): + 1112
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 207
  • No. + of tool users (all time) - all main servers: 6273
  • Tool + usage (5 years) - all main servers: 19
  • Tool usage (all + time) - all main servers: 1132
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: lca_wrapper + - description_md: '
  • Galaxy tool ids: legsta
  • Description: + Performs in silico Legionella pneumophila sequence based typing.
  • bio.tool + id: legsta
  • bio.tool ids: legsta
  • biii: + nan
  • bio.tool name: legsta
  • bio.tool description: + Performs in silico Legionella pneumophila sequence based typing
  • EDAM + operation: Sequence analysis
  • EDAM topic: Public + health and epidemiology
  • Status: Up-to-date
  • Source: + https://github.com/tseemann/legsta
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: legsta
  • Date + of first commit of the suite: 2022-02-21
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/tseemann/legsta
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta
  • Galaxy + wrapper version: 0.5.1
  • Conda id: legsta
  • Conda + version: 0.5.1
  • EDAM operation (no superclasses): + Sequence analysis
  • EDAM topic (no superclasses): Public + health and epidemiology
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 92
  • No. of tool users (all time) (usegalaxy.eu): 92
  • Tool + usage (5 years) (usegalaxy.eu): 8
  • Tool usage (all time) + (usegalaxy.eu): 8
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 92
  • No. of tool users (all time) - all main + servers: 92
  • Tool usage (5 years) - all main servers: + 8
  • Tool usage (all time) - all main servers: 8
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: legsta + - description_md: '
  • Galaxy tool ids: lighter
  • Description: + Lighter is a kmer-based error correction method for whole genome sequencing + data
  • bio.tool id: lighter
  • bio.tool ids: + lighter
  • biii: nan
  • bio.tool name: Lighter
  • 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.
  • EDAM operation: k-mer + counting, Sequence read processing, Sequencing quality control, Sequencing error + detection
  • EDAM topic: Sequencing, Whole genome sequencing, + DNA, Genomics
  • Status: To update
  • Source: + https://github.com/mourisl/Lighter
  • ToolShed categories: + Sequence Analysis, Fasta Manipulation
  • ToolShed id: lighter
  • Date + of first commit of the suite: 2016-06-04
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/lighter
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/lighter
  • Galaxy + wrapper version: 1.0
  • Conda id: lighter
  • Conda + version: 1.1.3
  • EDAM operation (no superclasses): + k-mer counting, Sequence read processing, Sequencing quality control, Sequencing + error detection
  • EDAM topic (no superclasses): Whole genome + sequencing, DNA, Genomics
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 149
  • No. of tool users (all time) (usegalaxy.eu): 171
  • Tool + usage (5 years) (usegalaxy.eu): 27
  • Tool usage (all time) + (usegalaxy.eu): 30
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 149
  • No. of tool users (all time) - all main + servers: 171
  • Tool usage (5 years) - all main servers: + 27
  • Tool usage (all time) - all main servers: 30
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: lighter + - description_md: '
  • Galaxy tool ids: limma_voom
  • Description: + Perform RNA-Seq differential expression analysis using limma voom pipeline
  • bio.tool + id: limma
  • bio.tool ids: limma
  • biii: + nan
  • bio.tool name: limma
  • bio.tool description: + Data analysis, linear models and differential expression for microarray data.
  • EDAM + operation: RNA-Seq analysis
  • EDAM topic: Molecular + biology, Genetics
  • Status: Up-to-date
  • Source: + http://bioconductor.org/packages/release/bioc/html/limma.html
  • ToolShed + categories: Transcriptomics, RNA, Statistics
  • ToolShed id: + limma_voom
  • Date of first commit of the suite: 2019-02-17
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom
  • Galaxy + wrapper version: 3.58.1
  • Conda id: bioconductor-limma
  • Conda + version: 3.58.1
  • EDAM operation (no superclasses): + RNA-Seq analysis
  • EDAM topic (no superclasses): Molecular + biology, Genetics
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 23442
  • No. of tool + users (all time) (usegalaxy.eu): 24466
  • Tool usage (5 years) + (usegalaxy.eu): 2379
  • Tool usage (all time) (usegalaxy.eu): + 2475
  • No. of tool users (5 years) (usegalaxy.org): 45734
  • No. + of tool users (all time) (usegalaxy.org): 49342
  • Tool usage + (5 years) (usegalaxy.org): 4565
  • Tool usage (all time) (usegalaxy.org): + 5032
  • No. of tool users (5 years) (usegalaxy.org.au): 9327
  • No. + of tool users (all time) (usegalaxy.org.au): 9517
  • Tool + usage (5 years) (usegalaxy.org.au): 835
  • Tool usage (all + time) (usegalaxy.org.au): 842
  • No. of tool users (5 years) + - all main servers: 78503
  • No. of tool users (all time) + - all main servers: 83325
  • Tool usage (5 years) - all main + servers: 7779
  • Tool usage (all time) - all main servers: + 8349
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: limma_voom + - description_md: '
  • Galaxy tool ids: lineagespot
  • Description: + Identification of SARS-CoV-2 related metagenomic mutations based on a single + (or a list of) variant(s) file(s)
  • bio.tool id: lineagespot
  • bio.tool + ids: lineagespot
  • biii: nan
  • bio.tool + name: lineagespot
  • 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).
  • EDAM + operation: Variant calling
  • EDAM topic: Metagenomics, + Gene transcripts, Evolutionary biology, Sequencing, Genetic variation
  • Status: + To update
  • Source: https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html
  • ToolShed + categories: Metagenomics, Sequence Analysis
  • ToolShed id: + lineagespot
  • Date of first commit of the suite: 2023-07-05
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot
  • Galaxy + wrapper version: 1.6.0
  • Conda id: r-base
  • Conda + version: nan
  • EDAM operation (no superclasses): Variant + calling
  • EDAM topic (no superclasses): Metagenomics, Gene + transcripts, Evolutionary biology, Sequencing, Genetic variation
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 39
  • No. of tool + users (all time) (usegalaxy.eu): 39
  • Tool usage (5 years) + (usegalaxy.eu): 4
  • Tool usage (all time) (usegalaxy.eu): + 4
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 39
  • No. + of tool users (all time) - all main servers: 39
  • Tool usage + (5 years) - all main servers: 4
  • Tool usage (all time) - + all main servers: 4
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: lineagespot + - description_md: '
  • Galaxy tool ids: lorikeet_spoligotype
  • Description: + Tools for M. tuberculosis DNA fingerprinting (spoligotyping)
  • bio.tool + id: lorikeet
  • bio.tool ids: lorikeet
  • biii: + nan
  • bio.tool name: lorikeet
  • bio.tool description: + Tools for M. tuberculosis DNA fingerprinting (spoligotyping)
  • EDAM + operation: Sequence analysis, Genotyping
  • EDAM topic: + Genotype and phenotype
  • Status: Up-to-date
  • Source: + https://github.com/AbeelLab/lorikeet
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: lorikeet_spoligotype
  • Date + of first commit of the suite: 2018-05-07
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/AbeelLab/lorikeet
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet
  • Galaxy + wrapper version: 20
  • Conda id: lorikeet
  • Conda + version: 20
  • EDAM operation (no superclasses): Sequence + analysis, Genotyping
  • EDAM topic (no superclasses): Genotype + and phenotype
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 822
  • No. of tool + users (all time) (usegalaxy.eu): 822
  • Tool usage (5 years) + (usegalaxy.eu): 14
  • Tool usage (all time) (usegalaxy.eu): + 14
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 822
  • No. + of tool users (all time) - all main servers: 822
  • Tool usage + (5 years) - all main servers: 14
  • Tool usage (all time) + - all main servers: 14
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: lorikeet + - description_md: '
  • Galaxy tool ids: lotus2
  • Description: + LotuS2 OTU processing pipeline
  • bio.tool id: lotus2
  • bio.tool + ids: lotus2
  • biii: nan
  • bio.tool name: + lotus2
  • 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.
  • EDAM operation: Sequence feature detection, + DNA barcoding
  • EDAM topic: Metagenomics, Taxonomy, Microbial + ecology
  • Status: To update
  • Source: + http://lotus2.earlham.ac.uk/
  • ToolShed categories: Metagenomics
  • ToolShed + id: lotus2
  • Date of first commit of the suite: 2021-06-08
  • Galaxy + wrapper owner: earlhaminst
  • Galaxy wrapper source: + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2
  • Galaxy + wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2
  • Galaxy + wrapper version: 2.32
  • Conda id: lotus2
  • Conda + version: 2.34.1
  • EDAM operation (no superclasses): + Sequence feature detection, DNA barcoding
  • EDAM topic (no superclasses): + Metagenomics, Taxonomy, Microbial ecology
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1219
  • No. of tool users (all time) (usegalaxy.eu): 1219
  • Tool + usage (5 years) (usegalaxy.eu): 182
  • Tool usage (all time) + (usegalaxy.eu): 182
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 37
  • No. of tool users (all time) (usegalaxy.org.au): 37
  • Tool + usage (5 years) (usegalaxy.org.au): 4
  • Tool usage (all time) + (usegalaxy.org.au): 4
  • No. of tool users (5 years) - all + main servers: 1256
  • No. of tool users (all time) - all main + servers: 1256
  • Tool usage (5 years) - all main servers: + 186
  • Tool usage (all time) - all main servers: 186
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: lotus2 + - description_md: '
  • Galaxy tool ids: m6anet
  • Description: + m6anet to detect m6A RNA modifications from nanopore data
  • bio.tool + id: m6Anet
  • bio.tool ids: m6Anet
  • biii: + nan
  • bio.tool name: m6Anet
  • bio.tool description: + Detection of m6A from direct RNA sequencing using a Multiple Instance Learning + framework.
  • EDAM operation: Quantification, Imputation, + Gene expression profiling
  • EDAM topic: RNA-Seq, Transcriptomics, + RNA, Machine learning
  • Status: Up-to-date
  • Source: + https://m6anet.readthedocs.io/en/latest
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: m6anet
  • Date + of first commit of the suite: 2023-10-25
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet
  • Galaxy + wrapper version: 2.1.0
  • Conda id: m6anet
  • Conda + version: 2.1.0
  • EDAM operation (no superclasses): + Quantification, Imputation, Gene expression profiling
  • EDAM topic + (no superclasses): RNA-Seq, Transcriptomics, RNA, Machine learning
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 44
  • No. of tool + users (all time) (usegalaxy.eu): 44
  • Tool usage (5 years) + (usegalaxy.eu): 11
  • Tool usage (all time) (usegalaxy.eu): + 11
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 44
  • No. + of tool users (all time) - all main servers: 44
  • Tool usage + (5 years) - all main servers: 11
  • Tool usage (all time) + - all main servers: 11
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: m6anet + - description_md: "
  • Galaxy tool ids: maaslin2
  • Description:\ + \ MaAsLin2 is comprehensive R package for efficiently determining multivariable\ + \ association between microbial meta'omic features and clinical metadata.
  • bio.tool\ + \ id: maaslin2
  • bio.tool ids: maaslin2
  • biii:\ + \ nan
  • bio.tool name: MaAsLin2
  • 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.
  • EDAM operation: Filtering, Statistical calculation,\ + \ Standardisation and normalisation, Visualisation
  • EDAM topic:\ + \ Metagenomics, Statistics and probability
  • Status: Up-to-date
  • Source:\ + \ http://huttenhower.sph.harvard.edu/maaslin
  • ToolShed categories:\ + \ Metagenomics
  • ToolShed id: maaslin2
  • Date\ + \ of first commit of the suite: 2021-11-05
  • Galaxy wrapper\ + \ owner: iuc
  • Galaxy wrapper source: https://github.com/biobakery/Maaslin2
  • Galaxy\ + \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2
  • Galaxy\ + \ wrapper version: 1.18.0
  • Conda id: bioconductor-maaslin2
  • Conda\ + \ version: 1.18.0
  • EDAM operation (no superclasses):\ + \ Filtering, Standardisation and normalisation, Visualisation
  • EDAM\ + \ topic (no superclasses): Metagenomics, Statistics and probability
  • Available\ + \ on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au:\ + \ 0
  • Available on UseGalaxy.eu: 1
  • Available\ + \ on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main):\ + \ 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools\ + \ available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr:\ + \ 0
  • Tools available on APOSTL: 0
  • Tools available\ + \ on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools\ + \ available on ChemFlow: 0
  • Tools available on Coloc-stats:\ + \ 0
  • Tools available on CropGalaxy: 0
  • Tools\ + \ available on Dintor: 0
  • Tools available on GASLINI:\ + \ 0
  • Tools available on Galaxy@AuBi: 0
  • Tools\ + \ available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr:\ + \ 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools\ + \ available on GigaGalaxy: 0
  • Tools available on HyPhy HIV\ + \ NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite:\ + \ 0
  • Tools available on ImmPort Galaxy: 0
  • Tools\ + \ available on InteractoMIX: 0
  • Tools available on MISSISSIPPI:\ + \ 0
  • Tools available on Mandoiu Lab: 0
  • Tools\ + \ available on MiModD NacreousMap: 0
  • Tools available on\ + \ Oqtans: 0
  • Tools available on Palfinder: 0
  • Tools\ + \ available on PepSimili: 0
  • Tools available on PhagePromotor:\ + \ 0
  • Tools available on UseGalaxy.be: 0
  • Tools\ + \ available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no:\ + \ 0
  • Tools available on Viral Variant Visualizer (VVV):\ + \ 0
  • No. of tool users (5 years) (usegalaxy.eu): 2835
  • No.\ + \ of tool users (all time) (usegalaxy.eu): 2835
  • Tool usage\ + \ (5 years) (usegalaxy.eu): 59
  • Tool usage (all time) (usegalaxy.eu):\ + \ 59
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No.\ + \ of tool users (all time) (usegalaxy.org): 0
  • Tool usage\ + \ (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org):\ + \ 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No.\ + \ of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage\ + \ (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time)\ + \ (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all\ + \ main servers: 2835
  • No. of tool users (all time) - all\ + \ main servers: 2835
  • Tool usage (5 years) - all main servers:\ + \ 59
  • Tool usage (all time) - all main servers: 59
  • Reviewed:\ + \ True
  • To keep: True
  • Deprecated: False
" + title_md: maaslin2 + - description_md: '
  • Galaxy tool ids: rbc_mafft_add, rbc_mafft
  • Description: + Multiple alignment program for amino acid or nucleotide sequences
  • bio.tool + id: MAFFT
  • bio.tool ids: MAFFT
  • biii: + nan
  • bio.tool name: MAFFT
  • bio.tool description: + MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple + sequence alignment program.
  • EDAM operation: Multiple sequence + alignment
  • EDAM topic: Sequence analysis
  • Status: + To update
  • Source: https://mafft.cbrc.jp/alignment/software/
  • ToolShed + categories: RNA
  • ToolShed id: mafft
  • Date + of first commit of the suite: 2023-11-06
  • Galaxy wrapper + owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/mafft
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/mafft
  • Galaxy + wrapper version: 7.526
  • Conda id: mafft
  • Conda + version: 7.525
  • EDAM operation (no superclasses): + Multiple sequence alignment
  • EDAM topic (no superclasses): + Sequence analysis
  • Available on UseGalaxy.org (Main): 2
  • Available + on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: + 2
  • Available on UseGalaxy.fr: 2
  • Tools available + on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: + 2
  • Tools available on UseGalaxy.eu: 2
  • Tools + available on UseGalaxy.fr: 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: 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 172433
  • No. of tool + users (all time) (usegalaxy.eu): 174456
  • Tool usage (5 years) + (usegalaxy.eu): 1865
  • Tool usage (all time) (usegalaxy.eu): + 1951
  • No. of tool users (5 years) (usegalaxy.org): 108640
  • No. + of tool users (all time) (usegalaxy.org): 122790
  • Tool usage + (5 years) (usegalaxy.org): 4266
  • Tool usage (all time) (usegalaxy.org): + 5521
  • No. of tool users (5 years) (usegalaxy.org.au): 20027
  • No. + of tool users (all time) (usegalaxy.org.au): 20027
  • Tool + usage (5 years) (usegalaxy.org.au): 1172
  • Tool usage (all + time) (usegalaxy.org.au): 1172
  • No. of tool users (5 years) + - all main servers: 301100
  • No. of tool users (all time) + - all main servers: 317273
  • Tool usage (5 years) - all main + servers: 7303
  • Tool usage (all time) - all main servers: + 8644
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: mafft + - description_md: '
  • Galaxy tool ids: make_nr
  • Description: + Make a FASTA file non-redundant
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr
  • ToolShed + categories: Fasta Manipulation, Sequence Analysis
  • ToolShed + id: make_nr
  • Date of first commit of the suite: 2018-11-06
  • Galaxy + wrapper owner: peterjc
  • Galaxy wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr
  • Galaxy + wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr
  • Galaxy + wrapper version: 0.0.3
  • Conda id: biopython
  • Conda + version: 1.70
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: make_nr + - description_md: "
  • Galaxy tool ids: maker, maker_map_ids
  • 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.
  • bio.tool\ + \ id: maker
  • bio.tool ids: maker
  • biii:\ + \ nan
  • bio.tool name: MAKER
  • 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.
  • EDAM\ + \ operation: Genome annotation
  • EDAM topic: Genomics,\ + \ DNA, Sequence analysis
  • Status: To update
  • Source:\ + \ http://www.yandell-lab.org/software/maker.html
  • ToolShed categories:\ + \ Sequence Analysis
  • ToolShed id: nan
  • Date\ + \ of first commit of the suite: 2017-10-13
  • Galaxy wrapper\ + \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker
  • Galaxy\ + \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker
  • Galaxy\ + \ wrapper version: 2.31.11
  • Conda id: maker
  • Conda\ + \ version: 3.01.03
  • EDAM operation (no superclasses):\ + \ Genome annotation
  • EDAM topic (no superclasses): Genomics,\ + \ DNA, Sequence analysis
  • Available on UseGalaxy.org (Main):\ + \ 2
  • Available on UseGalaxy.org.au: 2
  • Available\ + \ on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr:\ + \ 2
  • Tools available on UseGalaxy.org (Main): 2
  • Tools\ + \ available on UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu:\ + \ 2
  • Tools available on UseGalaxy.fr: 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: 0
  • Tools available on IPK Galaxy Blast Suite:\ + \ 0
  • Tools available on ImmPort Galaxy: 0
  • Tools\ + \ available on InteractoMIX: 0
  • Tools available on MISSISSIPPI:\ + \ 0
  • Tools available on Mandoiu Lab: 0
  • Tools\ + \ available on MiModD NacreousMap: 0
  • Tools 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.no:\ + \ 2
  • Tools available on Viral Variant Visualizer (VVV):\ + \ 0
  • No. of tool users (5 years) (usegalaxy.eu): 6417
  • No.\ + \ of tool users (all time) (usegalaxy.eu): 6861
  • Tool usage\ + \ (5 years) (usegalaxy.eu): 1315
  • Tool usage (all time)\ + \ (usegalaxy.eu): 1366
  • No. of tool users (5 years) (usegalaxy.org):\ + \ 7235
  • No. of tool users (all time) (usegalaxy.org): 7235
  • Tool\ + \ usage (5 years) (usegalaxy.org): 1858
  • Tool usage (all\ + \ time) (usegalaxy.org): 1858
  • No. of tool users (5 years)\ + \ (usegalaxy.org.au): 4112
  • No. of tool users (all time)\ + \ (usegalaxy.org.au): 4112
  • Tool usage (5 years) (usegalaxy.org.au):\ + \ 902
  • Tool usage (all time) (usegalaxy.org.au): 902
  • No.\ + \ of tool users (5 years) - all main servers: 17764
  • No.\ + \ of tool users (all time) - all main servers: 18208
  • Tool\ + \ usage (5 years) - all main servers: 4075
  • Tool usage (all\ + \ time) - all main servers: 4126
  • Reviewed: True
  • To\ + \ keep: True
  • Deprecated: False
" + title_md: maker + - description_md: '
  • Galaxy tool ids: mapseq
  • Description: + fast and accurate sequence read classification tool designed to assign taxonomy + and OTU classifications to ribosomal RNA sequences.
  • bio.tool id: + mapseq
  • bio.tool ids: mapseq
  • biii: + nan
  • bio.tool name: MAPseq
  • bio.tool description: + Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis + .
  • EDAM operation: k-mer counting
  • EDAM topic: + Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, + features and motifs
  • Status: To update
  • Source: + https://github.com/jfmrod/MAPseq
  • ToolShed categories: Metagenomics
  • ToolShed + id: mapseq
  • Date of first commit of the suite: 2023-08-02
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq
  • Galaxy + wrapper version: 2.1.1b
  • Conda id: perl
  • Conda + version: nan
  • EDAM operation (no superclasses): k-mer + counting
  • EDAM topic (no superclasses): Functional, regulatory + and non-coding RNA, Sequence analysis, Sequence sites, features and motifs
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 7871
  • No. of tool + users (all time) (usegalaxy.eu): 7871
  • Tool usage (5 years) + (usegalaxy.eu): 32
  • Tool usage (all time) (usegalaxy.eu): + 32
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 7871
  • No. + of tool users (all time) - all main servers: 7871
  • Tool + usage (5 years) - all main servers: 32
  • Tool usage (all + time) - all main servers: 32
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: mapseq + - description_md: '
  • Galaxy tool ids: mash_screen, mash_sketch
  • Description: + Fast genome and metagenome distance estimation using MinHash
  • bio.tool + id: mash
  • bio.tool ids: mash
  • biii: + nan
  • bio.tool name: Mash
  • bio.tool description: + Fast genome and metagenome distance estimation using MinHash.
  • EDAM + operation: Sequence distance matrix generation
  • EDAM topic: + Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation
  • Status: + Up-to-date
  • Source: https://github.com/marbl/Mash
  • ToolShed + categories: Metagenomics
  • ToolShed id: nan
  • Date + of first commit of the suite: 2019-01-23
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash
  • Galaxy + wrapper version: 2.3
  • Conda id: mash
  • Conda + version: 2.3
  • EDAM operation (no superclasses): Sequence + distance matrix generation
  • EDAM topic (no superclasses): + Metagenomics, Statistics and probability, Sequence analysis, DNA mutation
  • Available + on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: + 2
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: + 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 10119
  • No. of tool + users (all time) (usegalaxy.eu): 10119
  • Tool usage (5 years) + (usegalaxy.eu): 61
  • Tool usage (all time) (usegalaxy.eu): + 61
  • No. of tool users (5 years) (usegalaxy.org): 19
  • No. + of tool users (all time) (usegalaxy.org): 19
  • Tool usage + (5 years) (usegalaxy.org): 9
  • Tool usage (all time) (usegalaxy.org): + 9
  • No. of tool users (5 years) (usegalaxy.org.au): 647
  • No. + of tool users (all time) (usegalaxy.org.au): 647
  • Tool usage + (5 years) (usegalaxy.org.au): 7
  • Tool usage (all time) (usegalaxy.org.au): + 7
  • No. of tool users (5 years) - all main servers: 10785
  • No. + of tool users (all time) - all main servers: 10785
  • Tool + usage (5 years) - all main servers: 77
  • Tool usage (all + time) - all main servers: 77
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: mash + - description_md: '
  • Galaxy tool ids: maxbin2
  • Description: + clusters metagenomic contigs into bins
  • bio.tool id: maxbin
  • bio.tool + ids: maxbin
  • biii: nan
  • bio.tool name: + MaxBin
  • bio.tool description: Software for binning assembled + metagenomic sequences based on an Expectation-Maximization algorithm.
  • EDAM + operation: Sequence assembly
  • EDAM topic: Metagenomics, + Sequence assembly, Microbiology
  • Status: To update
  • Source: + https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html
  • ToolShed + categories: Metagenomics
  • ToolShed id: maxbin2
  • Date + of first commit of the suite: 2019-10-24
  • Galaxy wrapper + owner: mbernt
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2
  • Galaxy + wrapper version: nan
  • Conda id: maxbin2
  • Conda + version: 2.2.7
  • EDAM operation (no superclasses): + Sequence assembly
  • EDAM topic (no superclasses): Metagenomics, + Sequence assembly, Microbiology
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 2798
  • No. of tool users (all time) (usegalaxy.eu): 2798
  • Tool + usage (5 years) (usegalaxy.eu): 314
  • Tool usage (all time) + (usegalaxy.eu): 314
  • No. of tool users (5 years) (usegalaxy.org): + 2452
  • No. of tool users (all time) (usegalaxy.org): 2452
  • Tool + usage (5 years) (usegalaxy.org): 508
  • Tool usage (all time) + (usegalaxy.org): 508
  • No. of tool users (5 years) (usegalaxy.org.au): + 914
  • No. of tool users (all time) (usegalaxy.org.au): 914
  • Tool + usage (5 years) (usegalaxy.org.au): 89
  • Tool usage (all + time) (usegalaxy.org.au): 89
  • No. of tool users (5 years) + - all main servers: 6164
  • No. of tool users (all time) - + all main servers: 6164
  • Tool usage (5 years) - all main + servers: 911
  • Tool usage (all time) - all main servers: + 911
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: maxbin2 + - description_md: '
  • Galaxy tool ids: maxquant, maxquant_mqpar
  • Description: + wrapper for MaxQuant
  • bio.tool id: maxquant
  • bio.tool + ids: maxquant
  • biii: nan
  • bio.tool name: + MaxQuant
  • bio.tool description: Quantitative proteomics + software package designed for analyzing large mass-spectrometric data sets. + It is specifically aimed at high-resolution MS data.
  • EDAM operation: + Imputation, Visualisation, Protein quantification, Statistical calculation, + Standardisation and normalisation, Heat map generation, Clustering, Principal + component plotting
  • EDAM topic: Proteomics experiment, Proteomics, + Statistics and probability
  • Status: Up-to-date
  • Source: + https://www.maxquant.org/
  • ToolShed categories: Proteomics
  • ToolShed + id: maxquant
  • Date of first commit of the suite: + 2021-08-05
  • Galaxy wrapper owner: galaxyp
  • Galaxy + wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
  • Galaxy + wrapper version: 2.0.3.0
  • Conda id: maxquant
  • Conda + version: 2.0.3.0
  • EDAM operation (no superclasses): + Imputation, Visualisation, Protein quantification, Standardisation and normalisation, + Heat map generation, Clustering
  • EDAM topic (no superclasses): + Proteomics experiment, Proteomics, Statistics and probability
  • Available + on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: + 2
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 6863
  • No. of tool + users (all time) (usegalaxy.eu): 7021
  • Tool usage (5 years) + (usegalaxy.eu): 1251
  • Tool usage (all time) (usegalaxy.eu): + 1264
  • No. of tool users (5 years) (usegalaxy.org): 2798
  • No. + of tool users (all time) (usegalaxy.org): 2798
  • Tool usage + (5 years) (usegalaxy.org): 543
  • Tool usage (all time) (usegalaxy.org): + 543
  • No. of tool users (5 years) (usegalaxy.org.au): 3189
  • No. + of tool users (all time) (usegalaxy.org.au): 3189
  • Tool + usage (5 years) (usegalaxy.org.au): 352
  • Tool usage (all + time) (usegalaxy.org.au): 352
  • No. of tool users (5 years) + - all main servers: 12850
  • No. of tool users (all time) + - all main servers: 13008
  • Tool usage (5 years) - all main + servers: 2146
  • Tool usage (all time) - all main servers: + 2159
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: maxquant + - description_md: '
  • Galaxy tool ids: mcl
  • Description: + The Markov Cluster Algorithm, a cluster algorithm for graphs
  • bio.tool + id: mcl
  • bio.tool ids: mcl
  • biii: + nan
  • bio.tool name: MCL
  • bio.tool description: + MCL is a clustering algorithm widely used in bioinformatics and gaining traction + in other fields.
  • EDAM operation: Clustering, Network analysis, + Gene regulatory network analysis
  • EDAM topic: Molecular + interactions, pathways and networks
  • Status: Up-to-date
  • Source: + https://micans.org/mcl/man/mcl.html
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: mcl
  • Date of + first commit of the suite: 2022-05-12
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/mcl
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl
  • Galaxy + wrapper version: 22.282
  • Conda id: mcl
  • Conda + version: 22.282
  • EDAM operation (no superclasses): + Clustering, Gene regulatory network analysis
  • EDAM topic (no superclasses): + Molecular interactions, pathways and networks
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 35
  • No. of tool users (all time) (usegalaxy.eu): 35
  • Tool + usage (5 years) (usegalaxy.eu): 13
  • Tool usage (all time) + (usegalaxy.eu): 13
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 35
  • No. of tool users (all time) - all main + servers: 35
  • Tool usage (5 years) - all main servers: + 13
  • Tool usage (all time) - all main servers: 13
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: mcl + - description_md: '
  • Galaxy tool ids: medaka_consensus, medaka_consensus_pipeline, + medaka_snp, medaka_variant
  • Description: Sequence correction + provided by ONT Research
  • bio.tool id: medaka
  • bio.tool + ids: medaka
  • biii: nan
  • bio.tool name: + Medaka
  • 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.
  • EDAM operation: Base-calling, + Variant calling, Sequence assembly
  • EDAM topic: Sequence + assembly, Machine learning
  • Status: To update
  • Source: + https://github.com/nanoporetech/medaka
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: nan
  • Date of + first commit of the suite: 2020-08-24
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka
  • Galaxy + wrapper version: 1.7.2
  • Conda id: medaka
  • Conda + version: 2.0.1
  • EDAM operation (no superclasses): + Base-calling, Variant calling, Sequence assembly
  • EDAM topic (no + superclasses): Sequence assembly, Machine learning
  • Available + on UseGalaxy.org (Main): 3
  • Available on UseGalaxy.org.au: + 3
  • Available on UseGalaxy.eu: 3
  • Available + on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): + 3
  • Tools available on UseGalaxy.org.au: 3
  • Tools + available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: + 3
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 3
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 117975
  • No. of tool + users (all time) (usegalaxy.eu): 117975
  • Tool usage (5 years) + (usegalaxy.eu): 1693
  • Tool usage (all time) (usegalaxy.eu): + 1693
  • No. of tool users (5 years) (usegalaxy.org): 55063
  • No. + of tool users (all time) (usegalaxy.org): 55063
  • Tool usage + (5 years) (usegalaxy.org): 796
  • Tool usage (all time) (usegalaxy.org): + 796
  • No. of tool users (5 years) (usegalaxy.org.au): 9325
  • No. + of tool users (all time) (usegalaxy.org.au): 9325
  • Tool + usage (5 years) (usegalaxy.org.au): 639
  • Tool usage (all + time) (usegalaxy.org.au): 639
  • No. of tool users (5 years) + - all main servers: 182363
  • No. of tool users (all time) + - all main servers: 182363
  • Tool usage (5 years) - all main + servers: 3128
  • Tool usage (all time) - all main servers: + 3128
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: medaka + - description_md: '
  • Galaxy tool ids: megahit
  • Description: + An ultra-fast single-node solution for large and complex metagenomics assembly + via succinct de Bruijn graph.
  • bio.tool id: megahit
  • bio.tool + ids: megahit
  • biii: nan
  • bio.tool name: + MEGAHIT
  • 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.
  • EDAM operation: Genome + assembly
  • EDAM topic: Metagenomics, Sequencing, Ecology, + Sequence assembly
  • Status: Up-to-date
  • Source: + https://github.com/voutcn/megahit
  • ToolShed categories: + Sequence Analysis, Assembly, Metagenomics
  • ToolShed id: + megahit
  • Date of first commit of the suite: 2017-09-22
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit
  • Galaxy + wrapper version: 1.2.9
  • Conda id: megahit
  • Conda + version: 1.2.9
  • EDAM operation (no superclasses): + Genome assembly
  • EDAM topic (no superclasses): Metagenomics, + Sequencing, Sequence assembly
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 12692
  • No. of tool users (all time) (usegalaxy.eu): 13292
  • Tool + usage (5 years) (usegalaxy.eu): 1349
  • Tool usage (all time) + (usegalaxy.eu): 1400
  • No. of tool users (5 years) (usegalaxy.org): + 16645
  • No. of tool users (all time) (usegalaxy.org): 16645
  • Tool + usage (5 years) (usegalaxy.org): 2140
  • Tool usage (all time) + (usegalaxy.org): 2140
  • No. of tool users (5 years) (usegalaxy.org.au): + 6214
  • No. of tool users (all time) (usegalaxy.org.au): 6214
  • Tool + usage (5 years) (usegalaxy.org.au): 431
  • Tool usage (all + time) (usegalaxy.org.au): 431
  • No. of tool users (5 years) + - all main servers: 35551
  • No. of tool users (all time) + - all main servers: 36151
  • Tool usage (5 years) - all main + servers: 3920
  • Tool usage (all time) - all main servers: + 3971
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: megahit + - description_md: '
  • Galaxy tool ids: megahit_contig2fastg
  • Description: + A subprogram within the Megahit toolkit for converting contigs to assembly graphs + (fastg)
  • bio.tool id: megahit
  • bio.tool ids: + megahit
  • biii: nan
  • bio.tool name: MEGAHIT
  • 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.
  • EDAM + operation: Genome assembly
  • EDAM topic: Metagenomics, + Sequencing, Ecology, Sequence assembly
  • Status: To update
  • Source: + https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp
  • ToolShed + categories: Sequence Analysis, Assembly, Metagenomics
  • ToolShed + id: megahit_contig2fastg
  • Date of first commit of the suite: + 2018-11-09
  • Galaxy wrapper owner: iuc
  • Galaxy + wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg
  • Galaxy + wrapper version: 1.1.3
  • Conda id: megahit
  • Conda + version: 1.2.9
  • EDAM operation (no superclasses): + Genome assembly
  • EDAM topic (no superclasses): Metagenomics, + Sequencing, Sequence assembly
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 513
  • No. of tool users (all time) (usegalaxy.eu): 557
  • Tool + usage (5 years) (usegalaxy.eu): 152
  • Tool usage (all time) + (usegalaxy.eu): 155
  • No. of tool users (5 years) (usegalaxy.org): + 74
  • No. of tool users (all time) (usegalaxy.org): 74
  • Tool + usage (5 years) (usegalaxy.org): 35
  • Tool usage (all time) + (usegalaxy.org): 35
  • No. of tool users (5 years) (usegalaxy.org.au): + 10
  • No. of tool users (all time) (usegalaxy.org.au): 10
  • Tool + usage (5 years) (usegalaxy.org.au): 4
  • Tool usage (all time) + (usegalaxy.org.au): 4
  • No. of tool users (5 years) - all + main servers: 597
  • No. of tool users (all time) - all main + servers: 641
  • Tool usage (5 years) - all main servers: + 191
  • Tool usage (all time) - all main servers: 194
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: megahit_contig2fastg + - description_md: "
  • Galaxy tool ids: megan_blast2lca, megan_blast2rma,\ + \ megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor,\ + \ megan_sam2rma
  • 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).
  • bio.tool\ + \ id: megan
  • bio.tool ids: megan
  • biii:\ + \ nan
  • bio.tool name: MEGAN
  • 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.
  • EDAM\ + \ operation: Sequence analysis, Taxonomic classification
  • EDAM\ + \ topic: Sequence analysis
  • Status: To update
  • Source:\ + \ https://github.com/husonlab/megan-ce
  • ToolShed categories:\ + \ Sequence Analysis
  • ToolShed id: megan
  • Date\ + \ of first commit of the suite: 2021-11-24
  • Galaxy wrapper\ + \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan
  • Galaxy\ + \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan
  • Galaxy\ + \ wrapper version: 6.21.7
  • Conda id: megan
  • Conda\ + \ version: 6.25.9
  • EDAM operation (no superclasses):\ + \ Sequence analysis, Taxonomic classification
  • EDAM topic (no superclasses):\ + \ Sequence analysis
  • Available on UseGalaxy.org (Main):\ + \ 0
  • Available on UseGalaxy.org.au: 0
  • Available\ + \ on UseGalaxy.eu: 7
  • Available on UseGalaxy.fr:\ + \ 0
  • Tools available on UseGalaxy.org (Main): 0
  • Tools\ + \ available on UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu:\ + \ 7
  • Tools available on UseGalaxy.fr: 0
  • Tools\ + \ available on APOSTL: 0
  • Tools available on ARGs-OAP:\ + \ 0
  • Tools available on CIRM-CFBP: 0
  • Tools\ + \ available on ChemFlow: 0
  • Tools available on Coloc-stats:\ + \ 0
  • Tools available on CropGalaxy: 0
  • Tools\ + \ available on Dintor: 0
  • Tools available on GASLINI:\ + \ 0
  • Tools available on Galaxy@AuBi: 0
  • Tools\ + \ available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr:\ + \ 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools\ + \ available on GigaGalaxy: 0
  • Tools available on HyPhy HIV\ + \ NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite:\ + \ 0
  • Tools available on ImmPort Galaxy: 0
  • Tools\ + \ available on InteractoMIX: 0
  • Tools available on MISSISSIPPI:\ + \ 0
  • Tools available on Mandoiu Lab: 0
  • Tools\ + \ available on MiModD NacreousMap: 0
  • Tools available on\ + \ Oqtans: 0
  • Tools available 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.no:\ + \ 0
  • Tools available on Viral Variant Visualizer (VVV):\ + \ 0
  • No. of tool users (5 years) (usegalaxy.eu): 4130
  • No.\ + \ of tool users (all time) (usegalaxy.eu): 4130
  • Tool usage\ + \ (5 years) (usegalaxy.eu): 447
  • Tool usage (all time) (usegalaxy.eu):\ + \ 447
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No.\ + \ of tool users (all time) (usegalaxy.org): 0
  • Tool usage\ + \ (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org):\ + \ 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No.\ + \ of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage\ + \ (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time)\ + \ (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all\ + \ main servers: 4130
  • No. of tool users (all time) - all\ + \ main servers: 4130
  • Tool usage (5 years) - all main servers:\ + \ 447
  • Tool usage (all time) - all main servers: 447
  • Reviewed:\ + \ True
  • To keep: True
  • Deprecated: False
" + title_md: megan + - description_md: '
  • Galaxy tool ids: meningotype
  • Description: + Assign sequence type to N. meningitidis genome assemblies
  • bio.tool + id: meningotype
  • bio.tool ids: meningotype
  • biii: + nan
  • bio.tool name: meningotype
  • bio.tool description: + In silico typing of Neisseria meningitidis contigs.
  • EDAM operation: + Genotyping, Multilocus sequence typing
  • EDAM topic: Microbiology, + Genotype and phenotype
  • Status: Up-to-date
  • Source: + https://github.com/MDU-PHL/meningotype
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: meningotype
  • Date + of first commit of the suite: 2023-06-06
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype
  • Galaxy + wrapper version: 0.8.5
  • Conda id: meningotype
  • Conda + version: 0.8.5
  • EDAM operation (no superclasses): + Multilocus sequence typing
  • EDAM topic (no superclasses): + Microbiology, Genotype and phenotype
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: meningotype + - description_md: '
  • Galaxy tool ids: merqury, merquryplot
  • Description: + Merqury is a tool for evaluating genomes assemblies based of k-mer operations.
  • bio.tool + id: merqury
  • bio.tool ids: merqury
  • biii: + nan
  • bio.tool name: Merqury
  • 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.
  • EDAM operation: + Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly
  • EDAM + topic: Sequence assembly, Whole genome sequencing, Plant biology
  • Status: + Up-to-date
  • Source: https://github.com/marbl/merqury
  • ToolShed + categories: Assembly
  • ToolShed id: merqury
  • Date + of first commit of the suite: 2021-04-18
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury
  • Galaxy + wrapper version: 1.3
  • Conda id: merqury
  • Conda + version: 1.3
  • EDAM operation (no superclasses): Genome + assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly
  • EDAM + topic (no superclasses): Sequence assembly, Whole genome sequencing, + Plant biology
  • Available on UseGalaxy.org (Main): 2
  • Available + on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: + 2
  • Available on UseGalaxy.fr: 2
  • Tools available + on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: + 2
  • Tools available on UseGalaxy.eu: 2
  • Tools + available on UseGalaxy.fr: 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 3150
  • No. of tool + users (all time) (usegalaxy.eu): 3150
  • Tool usage (5 years) + (usegalaxy.eu): 477
  • Tool usage (all time) (usegalaxy.eu): + 477
  • No. of tool users (5 years) (usegalaxy.org): 730
  • No. + of tool users (all time) (usegalaxy.org): 730
  • Tool usage + (5 years) (usegalaxy.org): 196
  • Tool usage (all time) (usegalaxy.org): + 196
  • No. of tool users (5 years) (usegalaxy.org.au): 1183
  • No. + of tool users (all time) (usegalaxy.org.au): 1183
  • Tool + usage (5 years) (usegalaxy.org.au): 151
  • Tool usage (all + time) (usegalaxy.org.au): 151
  • No. of tool users (5 years) + - all main servers: 5063
  • No. of tool users (all time) - + all main servers: 5063
  • Tool usage (5 years) - all main + servers: 824
  • Tool usage (all time) - all main servers: + 824
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: merqury + - description_md: '
  • Galaxy tool ids: meryl_arithmetic_kmers, + meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, + meryl_print, meryl_trio_mode
  • Description: Meryl a k-mer + counter.
  • bio.tool id: meryl
  • bio.tool ids: + meryl
  • biii: nan
  • bio.tool name: Meryl
  • 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.
  • EDAM operation: + k-mer counting
  • EDAM topic: Whole genome sequencing, Genomics, + Sequence analysis, Sequencing
  • Status: Up-to-date
  • Source: + https://github.com/marbl/meryl
  • ToolShed categories: Assembly
  • ToolShed + id: meryl
  • Date of first commit of the suite: 2021-04-05
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl
  • Galaxy + wrapper version: 1.3
  • Conda id: merqury
  • Conda + version: 1.3
  • EDAM operation (no superclasses): k-mer + counting
  • EDAM topic (no superclasses): Whole genome sequencing, + Genomics, Sequence analysis
  • Available on UseGalaxy.org (Main): + 7
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 7
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: meryl + - description_md: '
  • Galaxy tool ids: metabat2_jgi_summarize_bam_contig_depths, + metabat2
  • 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.
  • bio.tool id: MetaBAT_2
  • bio.tool + ids: MetaBAT_2
  • biii: nan
  • bio.tool + name: MetaBAT 2
  • 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
  • EDAM operation: + Read binning, Sequence assembly, Genome annotation
  • EDAM topic: + Metagenomics, Sequence assembly, Metagenomic sequencing
  • Status: + To update
  • Source: https://bitbucket.org/berkeleylab/metabat/src/master/
  • ToolShed + categories: Metagenomics
  • ToolShed id: metabat2
  • Date + of first commit of the suite: 2022-01-28
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2
  • Galaxy + wrapper version: 2.15
  • Conda id: metabat2
  • Conda + version: 2.17
  • EDAM operation (no superclasses): + Read binning, Sequence assembly, Genome annotation
  • EDAM topic + (no superclasses): Metagenomics, Sequence assembly, Metagenomic sequencing
  • Available + on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 2
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 6135
  • No. of tool + users (all time) (usegalaxy.eu): 6135
  • Tool usage (5 years) + (usegalaxy.eu): 382
  • Tool usage (all time) (usegalaxy.eu): + 382
  • No. of tool users (5 years) (usegalaxy.org): 881
  • No. + of tool users (all time) (usegalaxy.org): 881
  • Tool usage + (5 years) (usegalaxy.org): 151
  • Tool usage (all time) (usegalaxy.org): + 151
  • No. of tool users (5 years) (usegalaxy.org.au): 1094
  • No. + of tool users (all time) (usegalaxy.org.au): 1094
  • Tool + usage (5 years) (usegalaxy.org.au): 104
  • Tool usage (all + time) (usegalaxy.org.au): 104
  • No. of tool users (5 years) + - all main servers: 8110
  • No. of tool users (all time) - + all main servers: 8110
  • Tool usage (5 years) - all main + servers: 637
  • Tool usage (all time) - all main servers: + 637
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: metabat2 + - description_md: '
  • Galaxy tool ids: metaeuk_easy_predict
  • 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.
  • bio.tool + id: MetaEuk
  • bio.tool ids: MetaEuk
  • biii: + nan
  • bio.tool name: MetaEuk
  • bio.tool description: + MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale + eukaryotic metagenomics
  • EDAM operation: Homology-based + gene prediction
  • EDAM topic: Metagenomics, Gene and protein + families
  • Status: To update
  • Source: + https://github.com/soedinglab/metaeuk
  • ToolShed categories: + Sequence Analysis, Genome annotation
  • ToolShed id: nan
  • Date + of first commit of the suite: 2020-08-04
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk
  • Galaxy + wrapper version: 7.bba0d80
  • Conda id: metaeuk
  • Conda + version: 6.a5d39d9
  • EDAM operation (no superclasses): + Homology-based gene prediction
  • EDAM topic (no superclasses): + Metagenomics, Gene and protein families
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 312
  • No. of tool users (all time) (usegalaxy.eu): 312
  • Tool + usage (5 years) (usegalaxy.eu): 40
  • Tool usage (all time) + (usegalaxy.eu): 40
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 312
  • No. of tool users (all time) - all main + servers: 312
  • Tool usage (5 years) - all main servers: + 40
  • Tool usage (all time) - all main servers: 40
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: metaeuk + - description_md: '
  • Galaxy tool ids: metagene_annotator
  • Description: + MetaGeneAnnotator gene-finding program for prokaryote and phage
  • bio.tool + id: metageneannotator
  • bio.tool ids: metageneannotator
  • biii: + nan
  • bio.tool name: MetaGeneAnnotator
  • bio.tool + description: Prokaryotic gene finding program from environmental genome + shotgun sequences or metagenomic sequences.
  • EDAM operation: + Sequence annotation
  • EDAM topic: Genomics, Model organisms, + Data submission, annotation and curation
  • Status: Up-to-date
  • Source: + http://metagene.nig.ac.jp/
  • ToolShed categories: Sequence + Analysis
  • ToolShed id: metagene_annotator
  • Date + of first commit of the suite: 2018-03-21
  • Galaxy wrapper + owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator
  • Galaxy + wrapper version: 1.0
  • Conda id: metagene_annotator
  • Conda + version: 1.0
  • EDAM operation (no superclasses): Sequence + annotation
  • EDAM topic (no superclasses): Genomics, Model + organisms, Data submission, annotation and curation
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 980
  • No. of tool + users (all time) (usegalaxy.eu): 980
  • Tool usage (5 years) + (usegalaxy.eu): 323
  • Tool usage (all time) (usegalaxy.eu): + 323
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 980
  • No. + of tool users (all time) - all main servers: 980
  • Tool usage + (5 years) - all main servers: 323
  • Tool usage (all time) + - all main servers: 323
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: metagene_annotator + - description_md: '
  • Galaxy tool ids: metagenomeseq_normalizaton
  • Description: + metagenomeSeq Normalization
  • bio.tool id: metagenomeseq
  • bio.tool + ids: metagenomeseq
  • biii: nan
  • bio.tool + name: metagenomeSeq
  • 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.
  • EDAM operation: Sequence visualisation, + Statistical calculation
  • EDAM topic: Metagenomics, Sequencing
  • Status: + To update
  • Source: https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html
  • ToolShed + categories: Metagenomics
  • ToolShed id: metagenomeseq_normalization
  • Date + of first commit of the suite: 2017-03-27
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq
  • Galaxy + wrapper version: 1.16.0-0.0.1
  • Conda id: bioconductor-metagenomeseq
  • Conda + version: 1.43.0
  • EDAM operation (no superclasses): + Sequence visualisation, Statistical calculation
  • EDAM topic (no + superclasses): Metagenomics, Sequencing
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 556
  • No. of tool users (all time) (usegalaxy.eu): 756
  • Tool + usage (5 years) (usegalaxy.eu): 17
  • Tool usage (all time) + (usegalaxy.eu): 21
  • No. of tool users (5 years) (usegalaxy.org): + 310
  • No. of tool users (all time) (usegalaxy.org): 514
  • Tool + usage (5 years) (usegalaxy.org): 35
  • Tool usage (all time) + (usegalaxy.org): 55
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 866
  • No. of tool users (all time) - all main + servers: 1270
  • Tool usage (5 years) - all main servers: + 52
  • Tool usage (all time) - all main servers: 76
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: metagenomeseq + - description_md: '
  • Galaxy tool ids: metanovo
  • Description: + Produce targeted databases for mass spectrometry analysis.
  • bio.tool + id: metanovo
  • bio.tool ids: metanovo
  • biii: + nan
  • bio.tool name: MetaNovo
  • bio.tool description: + An open-source pipeline for probabilistic peptide discovery in complex metaproteomic + datasets.
  • EDAM operation: Target-Decoy, de Novo sequencing, + Tag-based peptide identification, Protein identification, Expression analysis
  • EDAM + topic: Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, + Small molecules
  • Status: Up-to-date
  • Source: + https://github.com/uct-cbio/proteomics-pipelines
  • ToolShed categories: + Proteomics
  • ToolShed id: metanovo
  • Date of + first commit of the suite: 2022-03-29
  • Galaxy wrapper owner: + galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo
  • Galaxy + wrapper version: 1.9.4
  • Conda id: metanovo
  • Conda + version: 1.9.4
  • EDAM operation (no superclasses): + Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein + identification, Expression analysis
  • EDAM topic (no superclasses): + Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 4471
  • No. of tool + users (all time) (usegalaxy.eu): 4471
  • Tool usage (5 years) + (usegalaxy.eu): 29
  • Tool usage (all time) (usegalaxy.eu): + 29
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 4471
  • No. + of tool users (all time) - all main servers: 4471
  • Tool + usage (5 years) - all main servers: 29
  • Tool usage (all + time) - all main servers: 29
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: metanovo + - description_md: '
  • Galaxy tool ids: customize_metaphlan_database, + extract_metaphlan_database, merge_metaphlan_tables, metaphlan
  • Description: + MetaPhlAn for Metagenomic Phylogenetic Analysis
  • bio.tool id: + metaphlan
  • bio.tool ids: metaphlan
  • biii: + nan
  • bio.tool name: MetaPhlAn
  • bio.tool description: + Computational tool for profiling the composition of microbial communities from + metagenomic shotgun sequencing data.
  • EDAM operation: Nucleic + acid sequence analysis, Phylogenetic tree analysis
  • EDAM topic: + Metagenomics, Phylogenomics
  • Status: Up-to-date
  • Source: + https://github.com/biobakery/MetaPhlAn
  • ToolShed categories: + Metagenomics
  • ToolShed id: metaphlan
  • Date + of first commit of the suite: 2021-04-13
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan
  • Galaxy + wrapper version: 4.1.1
  • Conda id: metaphlan
  • Conda + version: 4.1.1
  • EDAM operation (no superclasses): + Nucleic acid sequence analysis
  • EDAM topic (no superclasses): + Metagenomics, Phylogenomics
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 2
  • Available + on UseGalaxy.eu: 4
  • Available on UseGalaxy.fr: 4
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu: + 4
  • Tools available on UseGalaxy.fr: 4
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 4
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 16629
  • No. of tool users (all time) (usegalaxy.eu): 16648
  • Tool + usage (5 years) (usegalaxy.eu): 1183
  • Tool usage (all time) + (usegalaxy.eu): 1187
  • No. of tool users (5 years) (usegalaxy.org): + 3983
  • No. of tool users (all time) (usegalaxy.org): 3983
  • Tool + usage (5 years) (usegalaxy.org): 572
  • Tool usage (all time) + (usegalaxy.org): 572
  • No. of tool users (5 years) (usegalaxy.org.au): + 4747
  • No. of tool users (all time) (usegalaxy.org.au): 4747
  • Tool + usage (5 years) (usegalaxy.org.au): 278
  • Tool usage (all + time) (usegalaxy.org.au): 278
  • No. of tool users (5 years) + - all main servers: 25359
  • No. of tool users (all time) + - all main servers: 25378
  • Tool usage (5 years) - all main + servers: 2033
  • Tool usage (all time) - all main servers: + 2037
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: metaphlan + - description_md: '
  • Galaxy tool ids: metaquantome_db, metaquantome_expand, + metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz
  • Description: + quantitative analysis of microbiome taxonomy and function
  • bio.tool + id: metaQuantome
  • bio.tool ids: metaQuantome
  • biii: + nan
  • bio.tool name: metaQuantome
  • 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.
  • EDAM + operation: Principal component visualisation, Visualisation, Functional + clustering, Query and retrieval, Differential protein expression analysis, Heat + map generation, Quantification, Indexing, Filtering, Statistical inference
  • EDAM + topic: Proteomics, Metatranscriptomics, Microbial ecology, Proteomics + experiment, Metagenomics
  • Status: Up-to-date
  • Source: + https://github.com/galaxyproteomics/metaquantome/
  • ToolShed categories: + Proteomics
  • ToolShed id: metaquantome
  • Date + of first commit of the suite: 2019-04-05
  • Galaxy wrapper + owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome
  • Galaxy + wrapper version: 2.0.2
  • Conda id: metaquantome
  • Conda + version: 2.0.2
  • EDAM operation (no superclasses): + Principal component visualisation, Functional clustering, Query and retrieval, + Heat map generation, Quantification, Indexing, Filtering, Statistical inference
  • EDAM + topic (no superclasses): Proteomics, Metatranscriptomics, Microbial ecology, + Proteomics experiment, Metagenomics
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 6
  • Available + on UseGalaxy.eu: 6
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 6
  • Tools available on UseGalaxy.eu: + 6
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools 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.no: 6
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 2730
  • No. of tool users (all time) (usegalaxy.eu): 2831
  • Tool + usage (5 years) (usegalaxy.eu): 260
  • Tool usage (all time) + (usegalaxy.eu): 262
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 1540
  • No. of tool users (all time) (usegalaxy.org.au): 1540
  • Tool + usage (5 years) (usegalaxy.org.au): 71
  • Tool usage (all + time) (usegalaxy.org.au): 71
  • No. of tool users (5 years) + - all main servers: 4270
  • No. of tool users (all time) - + all main servers: 4371
  • Tool usage (5 years) - all main + servers: 331
  • Tool usage (all time) - all main servers: + 333
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: metaquantome + - description_md: '
  • Galaxy tool ids: metawrapmg_binning
  • Description: + A flexible pipeline for genome-resolved metagenomic data analysis
  • bio.tool + id: metawrap
  • bio.tool ids: metawrap
  • biii: + nan
  • bio.tool name: MetaWRAP
  • 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.
  • EDAM operation: Read binning, + Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing
  • EDAM + topic: Whole genome sequencing, Metagenomic sequencing, Metagenomics
  • Status: + Up-to-date
  • Source: https://github.com/bxlab/metaWRAP
  • ToolShed + categories: Metagenomics
  • ToolShed id: metawrapmg_binning
  • Date + of first commit of the suite: 2024-04-11
  • Galaxy wrapper + owner: galaxy-australia
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg
  • Galaxy + wrapper version: 1.3.0
  • Conda id: metawrap-mg
  • Conda + version: 1.3.0
  • EDAM operation (no superclasses): + Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing
  • EDAM + topic (no superclasses): Whole genome sequencing, Metagenomic sequencing, + Metagenomics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 142
  • No. of tool + users (all time) (usegalaxy.eu): 142
  • Tool usage (5 years) + (usegalaxy.eu): 32
  • Tool usage (all time) (usegalaxy.eu): + 32
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 379
  • No. + of tool users (all time) (usegalaxy.org.au): 379
  • Tool usage + (5 years) (usegalaxy.org.au): 47
  • Tool usage (all time) + (usegalaxy.org.au): 47
  • No. of tool users (5 years) - all + main servers: 521
  • No. of tool users (all time) - all main + servers: 521
  • Tool usage (5 years) - all main servers: + 79
  • Tool usage (all time) - all main servers: 79
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: metawrapmg + - description_md: '
  • Galaxy tool ids: minia
  • Description: + Short-read assembler based on a de Bruijn graph
  • bio.tool id: + minia
  • bio.tool ids: minia
  • biii: nan
  • bio.tool + name: Minia
  • 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.
  • EDAM operation: Genome assembly
  • EDAM + topic: Sequence assembly
  • Status: Up-to-date
  • Source: + https://gatb.inria.fr/software/minia/
  • ToolShed categories: + Assembly
  • ToolShed id: minia
  • Date of first + commit of the suite: 2020-04-08
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia
  • Galaxy + wrapper version: 3.2.6
  • Conda id: minia
  • Conda + version: 3.2.6
  • EDAM operation (no superclasses): + Genome assembly
  • EDAM topic (no superclasses): Sequence + assembly
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 7116
  • No. of tool + users (all time) (usegalaxy.eu): 7116
  • Tool usage (5 years) + (usegalaxy.eu): 256
  • Tool usage (all time) (usegalaxy.eu): + 256
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 278
  • No. + of tool users (all time) (usegalaxy.org.au): 278
  • Tool usage + (5 years) (usegalaxy.org.au): 60
  • Tool usage (all time) + (usegalaxy.org.au): 60
  • No. of tool users (5 years) - all + main servers: 7394
  • No. of tool users (all time) - all main + servers: 7394
  • Tool usage (5 years) - all main servers: + 316
  • Tool usage (all time) - all main servers: 316
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: minia + - description_md: '
  • Galaxy tool ids: miniasm
  • Description: + Miniasm - Ultrafast de novo assembly for long noisy reads (though having no + consensus step)
  • bio.tool id: miniasm
  • bio.tool + ids: miniasm
  • biii: nan
  • bio.tool name: + miniasm
  • 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.
  • EDAM + operation: De-novo assembly
  • EDAM topic: Genomics, + Sequence assembly
  • Status: To update
  • Source: + https://github.com/lh3/miniasm
  • ToolShed categories: Assembly
  • ToolShed + id: miniasm
  • Date of first commit of the suite: 2019-06-18
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm
  • Galaxy + wrapper version: 0.3_r179
  • Conda id: miniasm
  • Conda + version: 0.3
  • EDAM operation (no superclasses): De-novo + assembly
  • EDAM topic (no superclasses): Genomics, Sequence + assembly
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 13357
  • No. of tool + users (all time) (usegalaxy.eu): 13479
  • Tool usage (5 years) + (usegalaxy.eu): 554
  • Tool usage (all time) (usegalaxy.eu): + 562
  • No. of tool users (5 years) (usegalaxy.org): 8416
  • No. + of tool users (all time) (usegalaxy.org): 8416
  • Tool usage + (5 years) (usegalaxy.org): 448
  • Tool usage (all time) (usegalaxy.org): + 448
  • No. of tool users (5 years) (usegalaxy.org.au): 898
  • No. + of tool users (all time) (usegalaxy.org.au): 898
  • Tool usage + (5 years) (usegalaxy.org.au): 85
  • Tool usage (all time) + (usegalaxy.org.au): 85
  • No. of tool users (5 years) - all + main servers: 22671
  • No. of tool users (all time) - all + main servers: 22793
  • Tool usage (5 years) - all main servers: + 1087
  • Tool usage (all time) - all main servers: 1095
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: miniasm + - description_md: '
  • Galaxy tool ids: minipolish
  • Description: + Polishing miniasm assemblies
  • bio.tool id: minipolish
  • bio.tool + ids: minipolish
  • biii: nan
  • bio.tool + name: minipolish
  • 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.
  • EDAM operation: Localised reassembly, Read + depth analysis
  • EDAM topic: Sequence assembly, Sequencing
  • Status: + Up-to-date
  • Source: https://github.com/rrwick/Minipolish
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: minipolish
  • Date + of first commit of the suite: 2022-10-19
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/minipolish
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/minipolish
  • Galaxy + wrapper version: 0.1.3
  • Conda id: minipolish
  • Conda + version: 0.1.3
  • EDAM operation (no superclasses): + Localised reassembly, Read depth analysis
  • EDAM topic (no superclasses): + Sequence assembly, Sequencing
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 229
  • No. of tool users (all time) (usegalaxy.eu): 229
  • Tool + usage (5 years) (usegalaxy.eu): 32
  • Tool usage (all time) + (usegalaxy.eu): 32
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 229
  • No. of tool users (all time) - all main + servers: 229
  • Tool usage (5 years) - all main servers: + 32
  • Tool usage (all time) - all main servers: 32
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: minipolish + - description_md: '
  • Galaxy tool ids: miniprot, miniprot_index
  • Description: + Align a protein sequence against a genome with affine gap penalty, splicing + and frameshift.
  • bio.tool id: miniprot
  • bio.tool + ids: miniprot
  • biii: nan
  • bio.tool name: + miniprot
  • 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.
  • EDAM operation: Sequence + alignment, Protein sequence analysis
  • EDAM topic: Sequence + sites, features and motifs, Sequence analysis
  • Status: Up-to-date
  • Source: + https://github.com/lh3/miniprot
  • ToolShed categories: Sequence + Analysis
  • ToolShed id: nan
  • Date of first commit + of the suite: 2023-03-23
  • Galaxy wrapper owner: iuc
  • Galaxy + wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot
  • Galaxy + wrapper version: 0.13
  • Conda id: miniprot
  • Conda + version: 0.13
  • EDAM operation (no superclasses): + Sequence alignment, Protein sequence analysis
  • EDAM topic (no superclasses): + Sequence sites, features and motifs, Sequence analysis
  • Available + on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 2
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1244
  • No. of tool + users (all time) (usegalaxy.eu): 1244
  • Tool usage (5 years) + (usegalaxy.eu): 86
  • Tool usage (all time) (usegalaxy.eu): + 86
  • No. of tool users (5 years) (usegalaxy.org): 24
  • No. + of tool users (all time) (usegalaxy.org): 24
  • Tool usage + (5 years) (usegalaxy.org): 15
  • Tool usage (all time) (usegalaxy.org): + 15
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1268
  • No. + of tool users (all time) - all main servers: 1268
  • Tool + usage (5 years) - all main servers: 101
  • Tool usage (all + time) - all main servers: 101
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: miniprot + - description_md: '
  • Galaxy tool ids: mitos, mitos2
  • Description: + de-novo annotation of metazoan mitochondrial genomes
  • bio.tool + id: mitos
  • bio.tool ids: mitos
  • biii: + nan
  • bio.tool name: MITOS
  • bio.tool description: + De novo metazoan mitochondrial genome annotation.
  • EDAM operation: + Genome annotation
  • EDAM topic: Zoology, Whole genome sequencing
  • Status: + To update
  • Source: http://mitos.bioinf.uni-leipzig.de/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: mitos
  • Date + of first commit of the suite: 2020-02-18
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos
  • Galaxy + wrapper version: 1.1.7
  • Conda id: mitos
  • Conda + version: 2.1.9
  • EDAM operation (no superclasses): + Genome annotation
  • EDAM topic (no superclasses): Zoology, + Whole genome sequencing
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 2
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 191295
  • No. of tool users (all time) (usegalaxy.eu): 191295
  • Tool + usage (5 years) (usegalaxy.eu): 1111
  • Tool usage (all time) + (usegalaxy.eu): 1111
  • No. of tool users (5 years) (usegalaxy.org): + 42265
  • No. of tool users (all time) (usegalaxy.org): 42265
  • Tool + usage (5 years) (usegalaxy.org): 320
  • Tool usage (all time) + (usegalaxy.org): 320
  • No. of tool users (5 years) (usegalaxy.org.au): + 10904
  • No. of tool users (all time) (usegalaxy.org.au): + 10904
  • Tool usage (5 years) (usegalaxy.org.au): 83
  • Tool + usage (all time) (usegalaxy.org.au): 83
  • No. of tool users + (5 years) - all main servers: 244464
  • No. of tool users + (all time) - all main servers: 244464
  • Tool usage (5 years) + - all main servers: 1514
  • Tool usage (all time) - all main + servers: 1514
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: mitos + - description_md: '
  • Galaxy tool ids: mlst, mlst_list
  • Description: + Scan contig files against PubMLST typing schemes
  • bio.tool id: + mlst
  • bio.tool ids: mlst
  • biii: nan
  • bio.tool + name: MLST
  • bio.tool description: Multi Locus Sequence + Typing from an assembled genome or from a set of reads.
  • EDAM operation: + Multilocus sequence typing
  • EDAM topic: Immunoproteins and + antigens
  • Status: To update
  • Source: + https://github.com/tseemann/mlst
  • ToolShed categories: Sequence + Analysis
  • ToolShed id: mlst
  • Date of first + commit of the suite: 2016-12-12
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst
  • Galaxy + wrapper version: 2.22.0
  • Conda id: mlst
  • Conda + version: 2.23.0
  • EDAM operation (no superclasses): + Multilocus sequence typing
  • EDAM topic (no superclasses): + Immunoproteins and antigens
  • Available on UseGalaxy.org (Main): + 2
  • Available on UseGalaxy.org.au: 2
  • Available + on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 2
  • Tools + available on UseGalaxy.org (Main): 2
  • Tools available on + UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu: + 2
  • Tools available on UseGalaxy.fr: 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: 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.no: 2
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 13300
  • No. of tool users (all time) (usegalaxy.eu): 13471
  • Tool + usage (5 years) (usegalaxy.eu): 1480
  • Tool usage (all time) + (usegalaxy.eu): 1501
  • No. of tool users (5 years) (usegalaxy.org): + 6532
  • No. of tool users (all time) (usegalaxy.org): 6532
  • Tool + usage (5 years) (usegalaxy.org): 1167
  • Tool usage (all time) + (usegalaxy.org): 1167
  • No. of tool users (5 years) (usegalaxy.org.au): + 10334
  • No. of tool users (all time) (usegalaxy.org.au): + 11841
  • Tool usage (5 years) (usegalaxy.org.au): 1083
  • Tool + usage (all time) (usegalaxy.org.au): 1300
  • No. of tool users + (5 years) - all main servers: 30166
  • No. of tool users (all + time) - all main servers: 31844
  • Tool usage (5 years) - + all main servers: 3730
  • Tool usage (all time) - all main + servers: 3968
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: mlst + - description_md: '
  • Galaxy tool ids: mob_recon, mob_typer
  • Description: + MOB-suite is a set of software tools for clustering, reconstruction and typing + of plasmids from draft assemblies
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://github.com/phac-nml/mob-suite
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: mob_suite
  • Date + of first commit of the suite: 2018-08-20
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/mob-suite
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite
  • Galaxy + wrapper version: 3.0.3
  • Conda id: mob_suite
  • Conda + version: 3.1.9
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 2
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 2
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: + 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 119024
  • No. of tool + users (all time) (usegalaxy.eu): 119024
  • Tool usage (5 years) + (usegalaxy.eu): 628
  • Tool usage (all time) (usegalaxy.eu): + 628
  • No. of tool users (5 years) (usegalaxy.org): 42
  • No. + of tool users (all time) (usegalaxy.org): 42
  • Tool usage + (5 years) (usegalaxy.org): 2
  • Tool usage (all time) (usegalaxy.org): + 2
  • No. of tool users (5 years) (usegalaxy.org.au): 36310
  • No. + of tool users (all time) (usegalaxy.org.au): 36310
  • Tool + usage (5 years) (usegalaxy.org.au): 191
  • Tool usage (all + time) (usegalaxy.org.au): 191
  • No. of tool users (5 years) + - all main servers: 155376
  • No. of tool users (all time) + - all main servers: 155376
  • Tool usage (5 years) - all main + servers: 821
  • Tool usage (all time) - all main servers: + 821
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: mob_suite + - description_md: '
  • 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
  • Description: + Mothur wrappers
  • bio.tool id: mothur
  • bio.tool + ids: mothur
  • biii: nan
  • bio.tool name: + mothur
  • bio.tool description: Open-source, platform-independent, + community-supported software for describing and comparing microbial communities
  • EDAM + operation: DNA barcoding, Sequencing quality control, Sequence clustering, + Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic + analysis
  • EDAM topic: Microbial ecology, Taxonomy, Sequence + analysis, Phylogeny
  • Status: To update
  • Source: + https://www.mothur.org
  • ToolShed categories: Metagenomics
  • ToolShed + id: mothur
  • Date of first commit of the suite: 2018-08-03
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur
  • Galaxy + wrapper version: 1.0
  • Conda id: mothur
  • Conda + version: 1.48.0
  • EDAM operation (no superclasses): + DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, + Visualisation, Sequence read processing, Phylogenetic analysis
  • EDAM + topic (no superclasses): Microbial ecology, Taxonomy, Sequence analysis, + Phylogeny
  • Available on UseGalaxy.org (Main): 129
  • Available + on UseGalaxy.org.au: 129
  • Available on UseGalaxy.eu: + 129
  • Available on UseGalaxy.fr: 129
  • Tools + available on UseGalaxy.org (Main): 129
  • Tools available + on UseGalaxy.org.au: 129
  • Tools available on UseGalaxy.eu: + 129
  • Tools available on UseGalaxy.fr: 129
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 129
  • Tools available on Viral + Variant Visualizer (VVV): 0
  • No. of tool users (5 years) + (usegalaxy.eu): 297546
  • No. of tool users (all time) (usegalaxy.eu): + 326056
  • Tool usage (5 years) (usegalaxy.eu): 37506
  • Tool + usage (all time) (usegalaxy.eu): 41763
  • No. of tool users + (5 years) (usegalaxy.org): 565218
  • No. of tool users (all + time) (usegalaxy.org): 682083
  • Tool usage (5 years) (usegalaxy.org): + 72163
  • Tool usage (all time) (usegalaxy.org): 89926
  • No. + of tool users (5 years) (usegalaxy.org.au): 167400
  • No. + of tool users (all time) (usegalaxy.org.au): 182490
  • Tool + usage (5 years) (usegalaxy.org.au): 26963
  • Tool usage (all + time) (usegalaxy.org.au): 28404
  • No. of tool users (5 years) + - all main servers: 1030164
  • No. of tool users (all time) + - all main servers: 1190629
  • Tool usage (5 years) - all + main servers: 136632
  • Tool usage (all time) - all main servers: + 160093
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: mothur + - description_md: '
  • Galaxy tool ids: mrbayes
  • Description: + A program for the Bayesian estimation of phylogeny.
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: nan
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: mrbayes
  • Date + of first commit of the suite: 2015-12-04
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: nan
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes
  • Galaxy + wrapper version: 1.0.2
  • Conda id: mrbayes
  • Conda + version: 3.2.7
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: mrbayes + - description_md: '
  • Galaxy tool ids: msconvert
  • Description: + msconvert Convert and/or filter mass spectrometry files (including vendor formats) + using the official Docker container
  • bio.tool id: msconvert
  • bio.tool + ids: msconvert
  • biii: nan
  • bio.tool + name: msConvert
  • 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.
  • EDAM + operation: Filtering, Formatting
  • EDAM topic: Proteomics, + Proteomics experiment
  • Status: To update
  • Source: + http://proteowizard.sourceforge.net/tools.shtml
  • ToolShed categories: + Proteomics
  • ToolShed id: msconvert
  • Date of + first commit of the suite: 2019-02-14
  • Galaxy wrapper owner: + galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
  • Galaxy + wrapper version: 3.0.20287
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): Filtering, + Formatting
  • EDAM topic (no superclasses): Proteomics, Proteomics + experiment
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 20749
  • No. of tool + users (all time) (usegalaxy.eu): 22184
  • Tool usage (5 years) + (usegalaxy.eu): 455
  • Tool usage (all time) (usegalaxy.eu): + 469
  • No. of tool users (5 years) (usegalaxy.org): 1239
  • No. + of tool users (all time) (usegalaxy.org): 1239
  • Tool usage + (5 years) (usegalaxy.org): 71
  • Tool usage (all time) (usegalaxy.org): + 71
  • No. of tool users (5 years) (usegalaxy.org.au): 2666
  • No. + of tool users (all time) (usegalaxy.org.au): 2666
  • Tool + usage (5 years) (usegalaxy.org.au): 53
  • Tool usage (all + time) (usegalaxy.org.au): 53
  • No. of tool users (5 years) + - all main servers: 24654
  • No. of tool users (all time) + - all main servers: 26089
  • Tool usage (5 years) - all main + servers: 579
  • Tool usage (all time) - all main servers: + 593
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: msconvert + - description_md: '
  • Galaxy tool ids: msstatstmt
  • Description: + MSstatsTMT protein significance analysis in shotgun mass spectrometry-based + proteomic experiments with tandem mass tag (TMT) labeling
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: http://msstats.org/msstatstmt/
  • ToolShed + categories: Proteomics
  • ToolShed id: msstatstmt
  • Date + of first commit of the suite: 2021-02-26
  • Galaxy wrapper + owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt
  • Galaxy + wrapper version: 2.0.0
  • Conda id: bioconductor-msstatstmt
  • Conda + version: 2.10.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 795
  • No. of tool + users (all time) (usegalaxy.eu): 795
  • Tool usage (5 years) + (usegalaxy.eu): 104
  • Tool usage (all time) (usegalaxy.eu): + 104
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 461
  • No. + of tool users (all time) (usegalaxy.org.au): 461
  • Tool usage + (5 years) (usegalaxy.org.au): 12
  • Tool usage (all time) + (usegalaxy.org.au): 12
  • No. of tool users (5 years) - all + main servers: 1256
  • No. of tool users (all time) - all main + servers: 1256
  • Tool usage (5 years) - all main servers: + 116
  • Tool usage (all time) - all main servers: 116
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: msstatstmt + - description_md: '
  • Galaxy tool ids: multigsea
  • Description: + GSEA-based pathway enrichment analysis for multi-omics data
  • bio.tool + id: multiGSEA
  • bio.tool ids: multiGSEA
  • biii: + nan
  • bio.tool name: multiGSEA
  • 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.
  • EDAM + operation: Gene-set enrichment analysis, Aggregation, Pathway analysis
  • EDAM + topic: Metabolomics, Molecular interactions, pathways and networks, Proteomics, + Transcriptomics, Small molecules
  • Status: Up-to-date
  • Source: + https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html
  • ToolShed + categories: Transcriptomics, Proteomics, Statistics
  • ToolShed + id: multigsea
  • Date of first commit of the suite: + 2023-06-07
  • Galaxy wrapper owner: iuc
  • Galaxy + wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea
  • Galaxy + wrapper version: 1.12.0
  • Conda id: bioconductor-multigsea
  • Conda + version: 1.12.0
  • EDAM operation (no superclasses): + Gene-set enrichment analysis, Aggregation, Pathway analysis
  • EDAM + topic (no superclasses): Metabolomics, Molecular interactions, pathways + and networks, Proteomics, Transcriptomics, Small molecules
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 106
  • No. of tool + users (all time) (usegalaxy.eu): 106
  • Tool usage (5 years) + (usegalaxy.eu): 25
  • Tool usage (all time) (usegalaxy.eu): + 25
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 106
  • No. + of tool users (all time) - all main servers: 106
  • Tool usage + (5 years) - all main servers: 25
  • Tool usage (all time) + - all main servers: 25
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: multigsea + - description_md: '
  • Galaxy tool ids: multiqc
  • Description: + MultiQC aggregates results from bioinformatics analyses across many samples + into a single report
  • bio.tool id: multiqc
  • bio.tool + ids: multiqc
  • biii: nan
  • bio.tool name: + MultiQC
  • 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.
  • EDAM operation: Validation, Sequencing quality control
  • EDAM + topic: Sequencing, Bioinformatics, Sequence analysis, Genomics
  • Status: + To update
  • Source: http://multiqc.info/
  • ToolShed + categories: Fastq Manipulation, Statistics, Visualization
  • ToolShed + id: multiqc
  • Date of first commit of the suite: 2020-04-28
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc
  • Galaxy + wrapper version: 1.24.1
  • Conda id: multiqc
  • Conda + version: 1.25.1
  • EDAM operation (no superclasses): + Sequencing quality control
  • EDAM topic (no superclasses): + Sequencing, Bioinformatics, Sequence analysis, Genomics
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 182221
  • No. of tool + users (all time) (usegalaxy.eu): 192389
  • Tool usage (5 years) + (usegalaxy.eu): 19343
  • Tool usage (all time) (usegalaxy.eu): + 20494
  • No. of tool users (5 years) (usegalaxy.org): 163961
  • No. + of tool users (all time) (usegalaxy.org): 182413
  • Tool usage + (5 years) (usegalaxy.org): 26449
  • Tool usage (all time) + (usegalaxy.org): 29758
  • No. of tool users (5 years) (usegalaxy.org.au): + 40663
  • No. of tool users (all time) (usegalaxy.org.au): + 41855
  • Tool usage (5 years) (usegalaxy.org.au): 5974
  • Tool + usage (all time) (usegalaxy.org.au): 6157
  • No. of tool users + (5 years) - all main servers: 386845
  • No. of tool users + (all time) - all main servers: 416657
  • Tool usage (5 years) + - all main servers: 51766
  • Tool usage (all time) - all main + servers: 56409
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: multiqc + - description_md: '
  • Galaxy tool ids: mykrobe_predict
  • Description: + Antibiotic resistance predictions
  • bio.tool id: Mykrobe
  • bio.tool + ids: Mykrobe
  • biii: nan
  • bio.tool name: + Mykrobe
  • 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
  • EDAM + operation: Antimicrobial resistance prediction, Variant calling, Genotyping, + Sequence trimming
  • EDAM topic: Whole genome sequencing, + Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics
  • Status: + To update
  • Source: https://github.com/Mykrobe-tools/mykrobe
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: mykrobe
  • Date + of first commit of the suite: 2017-12-18
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe
  • Galaxy + wrapper version: 0.10.0
  • Conda id: mykrobe
  • Conda + version: 0.13.0
  • EDAM operation (no superclasses): + Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming
  • EDAM + topic (no superclasses): Whole genome sequencing, Genotype and phenotype, + Probes and primers, Genetic variation, Metagenomics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: mykrobe + - description_md: '
  • Galaxy tool ids: mykrobe_parseR
  • Description: + RScript to parse the results of mykrobe predictor.
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: https://github.com/phac-nml/mykrobe-parser
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: mykrobe_parser
  • Date + of first commit of the suite: 2018-09-28
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/mykrobe-parser
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser
  • Galaxy + wrapper version: 0.1.4.1
  • Conda id: r-base
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: mykrobe_parser + - description_md: '
  • Galaxy tool ids: mz_to_sqlite
  • Description: + Creates a SQLite database for proteomics data
  • bio.tool id: + mztosqlite
  • bio.tool ids: mztosqlite
  • biii: + nan
  • bio.tool name: mzToSQLite
  • bio.tool description: + Convert proteomics data files into a SQLite database
  • EDAM operation: + Conversion, Peptide database search
  • EDAM topic: Proteomics, + Biological databases
  • Status: To update
  • Source: + https://github.com/galaxyproteomics/mzToSQLite
  • ToolShed categories: + Proteomics
  • ToolShed id: mz_to_sqlite
  • Date + of first commit of the suite: 2015-06-01
  • Galaxy wrapper + owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite
  • Galaxy + wrapper version: 2.1.1+galaxy0
  • Conda id: mztosqlite
  • Conda + version: 2.1.1
  • EDAM operation (no superclasses): + Conversion, Peptide database search
  • EDAM topic (no superclasses): + Proteomics, Biological databases
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 854
  • No. of tool users (all time) (usegalaxy.eu): 860
  • Tool + usage (5 years) (usegalaxy.eu): 110
  • Tool usage (all time) + (usegalaxy.eu): 111
  • No. of tool users (5 years) (usegalaxy.org): + 79
  • No. of tool users (all time) (usegalaxy.org): 79
  • Tool + usage (5 years) (usegalaxy.org): 15
  • Tool usage (all time) + (usegalaxy.org): 15
  • No. of tool users (5 years) (usegalaxy.org.au): + 274
  • No. of tool users (all time) (usegalaxy.org.au): 274
  • Tool + usage (5 years) (usegalaxy.org.au): 13
  • Tool usage (all + time) (usegalaxy.org.au): 13
  • No. of tool users (5 years) + - all main servers: 1207
  • No. of tool users (all time) - + all main servers: 1213
  • Tool usage (5 years) - all main + servers: 138
  • Tool usage (all time) - all main servers: + 139
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: mz_to_sqlite + - description_md: '
  • Galaxy tool ids: nanocompore_db, nanocompore_sampcomp
  • 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.
  • bio.tool id: Nanocompore
  • bio.tool + ids: Nanocompore
  • biii: nan
  • bio.tool + name: Nanocompore
  • 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
  • EDAM + operation: Post-translation modification site prediction, 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
  • Status: To update
  • Source: + https://nanocompore.rna.rocks/
  • ToolShed categories: Sequence + Analysis
  • ToolShed id: nanocompore
  • Date of + first commit of the suite: 2020-05-01
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore
  • Galaxy + wrapper version: 1.0.0rc3.post2
  • Conda id: nanocompore
  • Conda + version: 1.0.4
  • EDAM operation (no superclasses): + PolyA signal detection, Genotyping, k-mer counting
  • EDAM topic + (no superclasses): Functional, regulatory and non-coding RNA, RNA-Seq, + Gene transcripts, Transcriptomics, Transcription factors and regulatory sites
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 839
  • No. of tool + users (all time) (usegalaxy.eu): 839
  • Tool usage (5 years) + (usegalaxy.eu): 12
  • Tool usage (all time) (usegalaxy.eu): + 12
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 269
  • No. + of tool users (all time) (usegalaxy.org.au): 269
  • Tool usage + (5 years) (usegalaxy.org.au): 5
  • Tool usage (all time) (usegalaxy.org.au): + 5
  • No. of tool users (5 years) - all main servers: 1108
  • No. + of tool users (all time) - all main servers: 1108
  • Tool + usage (5 years) - all main servers: 17
  • Tool usage (all + time) - all main servers: 17
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: nanocompore + - description_md: '
  • Galaxy tool ids: nanoplot
  • Description: + Plotting tool for long read sequencing data and alignments
  • bio.tool + id: nanoplot
  • bio.tool ids: nanoplot
  • biii: + nan
  • bio.tool name: NanoPlot
  • 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
  • EDAM + operation: Scatter plot plotting, Box-Whisker plot plotting
  • EDAM + topic: Genomics
  • Status: Up-to-date
  • Source: + https://github.com/wdecoster/NanoPlot
  • ToolShed categories: + Visualization
  • ToolShed id: nanoplot
  • Date + of first commit of the suite: 2018-09-28
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot
  • Galaxy + wrapper version: 1.43.0
  • Conda id: nanoplot
  • Conda + version: 1.43.0
  • EDAM operation (no superclasses): + Scatter plot plotting, Box-Whisker plot plotting
  • EDAM topic (no + superclasses): Genomics
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 99052
  • No. of tool users (all time) (usegalaxy.eu): 100009
  • Tool + usage (5 years) (usegalaxy.eu): 5671
  • Tool usage (all time) + (usegalaxy.eu): 5755
  • No. of tool users (5 years) (usegalaxy.org): + 40386
  • No. of tool users (all time) (usegalaxy.org): 40386
  • Tool + usage (5 years) (usegalaxy.org): 3371
  • Tool usage (all time) + (usegalaxy.org): 3371
  • No. of tool users (5 years) (usegalaxy.org.au): + 17919
  • No. of tool users (all time) (usegalaxy.org.au): + 17919
  • Tool usage (5 years) (usegalaxy.org.au): 2188
  • Tool + usage (all time) (usegalaxy.org.au): 2188
  • No. of tool users + (5 years) - all main servers: 157357
  • No. of tool users + (all time) - all main servers: 158314
  • Tool usage (5 years) + - all main servers: 11230
  • Tool usage (all time) - all main + servers: 11314
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: nanoplot + - description_md: '
  • Galaxy tool ids: nanopolishcomp_eventaligncollapse, + nanopolishcomp_freqmethcalculate
  • 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.
  • bio.tool + id: nanopolishcomp
  • bio.tool ids: nanopolishcomp
  • biii: + nan
  • bio.tool name: NanopolishComp
  • bio.tool + description: NanopolishComp is a Python3 package for downstream analyses + of Nanopolish output files.It is a companion package for Nanopolish.
  • EDAM + operation: Methylation analysis, Collapsing methods
  • EDAM + topic: Sequence analysis, Sequencing, Genetic variation
  • Status: + To update
  • Source: https://a-slide.github.io/NanopolishComp
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: nanopolishcomp
  • Date + of first commit of the suite: 2020-04-27
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp
  • Galaxy + wrapper version: 0.6.11
  • Conda id: nanopolishcomp
  • Conda + version: 0.6.12
  • EDAM operation (no superclasses): + Methylation analysis, Collapsing methods
  • EDAM topic (no superclasses): + Sequence analysis, Sequencing, Genetic variation
  • Available on + UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1091
  • No. of tool + users (all time) (usegalaxy.eu): 1091
  • Tool usage (5 years) + (usegalaxy.eu): 44
  • Tool usage (all time) (usegalaxy.eu): + 44
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1091
  • No. + of tool users (all time) - all main servers: 1091
  • Tool + usage (5 years) - all main servers: 44
  • Tool usage (all + time) - all main servers: 44
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: nanopolishcomp + - description_md: '
  • Galaxy tool ids: blastxml_to_tabular, get_species_taxids, + ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, + ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, + ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, + ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, + ncbi_tblastx_wrapper
  • Description: NCBI BLAST+
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://blast.ncbi.nlm.nih.gov/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: ncbi_blast_plus
  • Date + of first commit of the suite: 2020-09-08
  • Galaxy wrapper + owner: devteam
  • Galaxy wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus
  • Galaxy + wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus
  • Galaxy + wrapper version: 2.14.1
  • Conda id: python
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 16
  • Available on UseGalaxy.org.au: 16
  • Available + on UseGalaxy.eu: 16
  • Available on UseGalaxy.fr: 16
  • Tools + available on UseGalaxy.org (Main): 16
  • Tools available on + UseGalaxy.org.au: 16
  • Tools available on UseGalaxy.eu: + 16
  • Tools available on UseGalaxy.fr: 16
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 16
  • Tools available on Galaxy@Pasteur: + 15
  • Tools available on GalaxyTrakr: 16
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 16
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 16
  • Tools + available on PhagePromotor: 15
  • Tools available on UseGalaxy.be: + 16
  • Tools available on UseGalaxy.cz: 16
  • Tools + available on UseGalaxy.no: 15
  • Tools available on Viral + Variant Visualizer (VVV): 0
  • No. of tool users (5 years) + (usegalaxy.eu): 391141
  • No. of tool users (all time) (usegalaxy.eu): + 443752
  • Tool usage (5 years) (usegalaxy.eu): 9760
  • Tool + usage (all time) (usegalaxy.eu): 10546
  • No. of tool users + (5 years) (usegalaxy.org): 306361
  • No. of tool users (all + time) (usegalaxy.org): 350178
  • Tool usage (5 years) (usegalaxy.org): + 11767
  • Tool usage (all time) (usegalaxy.org): 13684
  • No. + of tool users (5 years) (usegalaxy.org.au): 227235
  • No. + of tool users (all time) (usegalaxy.org.au): 244814
  • Tool + usage (5 years) (usegalaxy.org.au): 3192
  • Tool usage (all + time) (usegalaxy.org.au): 3617
  • No. of tool users (5 years) + - all main servers: 924737
  • No. of tool users (all time) + - all main servers: 1038744
  • Tool usage (5 years) - all + main servers: 24719
  • Tool usage (all time) - all main servers: + 27847
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: ncbi_blast_plus + - description_md: '
  • Galaxy tool ids: ncbi_fcs_gx
  • Description: + FCS-GX detects contamination from foreign organisms in genome sequences using + the genome cross-species aligner (GX).
  • bio.tool id: ncbi_fcs
  • bio.tool + ids: ncbi_fcs
  • biii: nan
  • bio.tool name: + NCBI fcs
  • 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.
  • EDAM operation: + Sequence assembly validation, Sequence trimming, Sequence contamination filtering
  • EDAM + topic: Sequence analysis, Sequence assembly
  • Status: + Up-to-date
  • Source: https://github.com/ncbi/fcs-gx
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: ncbi_fcs_gx
  • Date + of first commit of the suite: 2023-11-14
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx
  • Galaxy + wrapper version: 0.5.4
  • Conda id: ncbi-fcs-gx
  • Conda + version: 0.5.4
  • EDAM operation (no superclasses): + Sequence assembly validation, Sequence trimming, Sequence contamination filtering
  • EDAM + topic (no superclasses): Sequence analysis, Sequence assembly
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 125
  • No. of tool + users (all time) (usegalaxy.eu): 125
  • Tool usage (5 years) + (usegalaxy.eu): 26
  • Tool usage (all time) (usegalaxy.eu): + 26
  • No. of tool users (5 years) (usegalaxy.org): 2489
  • No. + of tool users (all time) (usegalaxy.org): 2489
  • Tool usage + (5 years) (usegalaxy.org): 139
  • Tool usage (all time) (usegalaxy.org): + 139
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 2614
  • No. + of tool users (all time) - all main servers: 2614
  • Tool + usage (5 years) - all main servers: 165
  • Tool usage (all + time) - all main servers: 165
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: ncbi_fcs_gx + - description_md: '
  • Galaxy tool ids: newick_display
  • Description: + Perform operations on Newick trees
  • bio.tool id: newick_utilities
  • bio.tool + ids: newick_utilities
  • biii: nan
  • bio.tool + name: Newick Utilities
  • 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.
  • EDAM operation: Phylogenetic tree generation, Phylogenetic + tree analysis, Phylogenetic tree reconstruction
  • EDAM topic: + Phylogeny, Genomics, Computer science
  • Status: To update
  • Source: + http://cegg.unige.ch/newick_utils
  • ToolShed categories: + Visualization, Metagenomics
  • ToolShed id: newick_utils
  • Date + of first commit of the suite: 2018-10-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/tjunier/newick_utils
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils
  • Galaxy + wrapper version: 1.6+galaxy1
  • Conda id: newick_utils
  • Conda + version: 1.6
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): Phylogeny, Genomics, Computer science
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 33637
  • No. of tool + users (all time) (usegalaxy.eu): 34195
  • Tool usage (5 years) + (usegalaxy.eu): 1113
  • Tool usage (all time) (usegalaxy.eu): + 1172
  • No. of tool users (5 years) (usegalaxy.org): 16257
  • No. + of tool users (all time) (usegalaxy.org): 16257
  • Tool usage + (5 years) (usegalaxy.org): 1816
  • Tool usage (all time) (usegalaxy.org): + 1816
  • No. of tool users (5 years) (usegalaxy.org.au): 7582
  • No. + of tool users (all time) (usegalaxy.org.au): 7582
  • Tool + usage (5 years) (usegalaxy.org.au): 899
  • Tool usage (all + time) (usegalaxy.org.au): 899
  • No. of tool users (5 years) + - all main servers: 57476
  • No. of tool users (all time) + - all main servers: 58034
  • Tool usage (5 years) - all main + servers: 3828
  • Tool usage (all time) - all main servers: + 3887
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: newick_utils + - description_md: '
  • Galaxy tool ids: nextalign, nextclade
  • Description: + Identify differences between your sequences and a reference sequence used by + Nextstrain
  • bio.tool id: nextclade
  • bio.tool + ids: nextclade
  • biii: nan
  • bio.tool + name: Nextclade
  • bio.tool description: Nextclade + is an open-source project for viral genome alignment, mutation calling, clade + assignment, quality checks and phylogenetic placement.
  • EDAM operation: + Methylation analysis, Variant calling
  • EDAM topic: Genomics, + Sequence analysis, Cladistics
  • Status: To update
  • Source: + https://github.com/nextstrain/nextclade
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: nan
  • Date of + first commit of the suite: 2021-04-26
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade
  • Galaxy + wrapper version: 2.7.0
  • Conda id: nextalign
  • Conda + version: 2.14.0
  • EDAM operation (no superclasses): + Methylation analysis, Variant calling
  • EDAM topic (no superclasses): + Genomics, Cladistics
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 2
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 2
  • Tools available on UseGalaxy.fr: 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: 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 4411
  • No. of tool users (all time) (usegalaxy.eu): 4411
  • Tool + usage (5 years) (usegalaxy.eu): 396
  • Tool usage (all time) + (usegalaxy.eu): 396
  • No. of tool users (5 years) (usegalaxy.org): + 9708
  • No. of tool users (all time) (usegalaxy.org): 9708
  • Tool + usage (5 years) (usegalaxy.org): 279
  • Tool usage (all time) + (usegalaxy.org): 279
  • No. of tool users (5 years) (usegalaxy.org.au): + 2099
  • No. of tool users (all time) (usegalaxy.org.au): 2099
  • Tool + usage (5 years) (usegalaxy.org.au): 212
  • Tool usage (all + time) (usegalaxy.org.au): 212
  • No. of tool users (5 years) + - all main servers: 16218
  • No. of tool users (all time) + - all main servers: 16218
  • Tool usage (5 years) - all main + servers: 887
  • Tool usage (all time) - all main servers: + 887
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: nextclade + - description_md: '
  • Galaxy tool ids: nextdenovo
  • Description: + String graph-based de novo assembler for long reads
  • bio.tool id: + nextdenovo
  • bio.tool ids: nextdenovo
  • biii: + nan
  • bio.tool name: NextDenovo
  • bio.tool description: + NextDenovo 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.
  • EDAM operation: De-novo assembly, Genome + assembly
  • EDAM topic: Sequencing, Sequence assembly
  • Status: + To update
  • Source: https://github.com/Nextomics/NextDenovo
  • ToolShed + categories: Assembly
  • ToolShed id: nextdenovo
  • Date + of first commit of the suite: 2023-02-09
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo
  • Galaxy + wrapper version: 2.5.0
  • Conda id: nextdenovo
  • Conda + version: 2.5.2
  • EDAM operation (no superclasses): + De-novo assembly, Genome assembly
  • EDAM topic (no superclasses): + Sequencing, Sequence assembly
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 391
  • No. of tool users (all time) (usegalaxy.eu): 391
  • Tool + usage (5 years) (usegalaxy.eu): 158
  • Tool usage (all time) + (usegalaxy.eu): 158
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 391
  • No. of tool users (all time) - all main + servers: 391
  • Tool usage (5 years) - all main servers: + 158
  • Tool usage (all time) - all main servers: 158
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: nextdenovo + - description_md: '
  • Galaxy tool ids: nonpareil
  • Description: + Estimate average coverage in metagenomic datasets
  • bio.tool id: + nonpareil
  • bio.tool ids: nonpareil
  • biii: + nan
  • bio.tool name: nonpareil
  • bio.tool description: + Estimate metagenomic coverage and sequence diversity
  • EDAM operation: + Operation
  • EDAM topic: nan
  • Status: + To update
  • Source: http://nonpareil.readthedocs.io
  • ToolShed + categories: Metagenomics
  • ToolShed id: nonpareil
  • Date + of first commit of the suite: 2017-11-03
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil
  • Galaxy + wrapper version: 3.1.1
  • Conda id: nonpareil
  • Conda + version: 3.5.5
  • EDAM operation (no superclasses): + Operation
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 107
  • No. of tool + users (all time) (usegalaxy.eu): 143
  • Tool usage (5 years) + (usegalaxy.eu): 13
  • Tool usage (all time) (usegalaxy.eu): + 15
  • No. of tool users (5 years) (usegalaxy.org): 148
  • No. + of tool users (all time) (usegalaxy.org): 148
  • Tool usage + (5 years) (usegalaxy.org): 20
  • Tool usage (all time) (usegalaxy.org): + 20
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 255
  • No. + of tool users (all time) - all main servers: 291
  • Tool usage + (5 years) - all main servers: 33
  • Tool usage (all time) + - all main servers: 35
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: nonpareil + - description_md: '
  • Galaxy tool ids: Nucleosome
  • Description: + Prediction of Nucleosomes Positions on the Genome
  • bio.tool id: + nucleosome_prediction
  • bio.tool ids: nucleosome_prediction
  • biii: + nan
  • bio.tool name: nucleosome_prediction
  • bio.tool + description: Prediction of Nucleosomes Positions on the Genome
  • EDAM + operation: Prediction and recognition, Nucleosome position prediction, + Sequence analysis
  • EDAM topic: Structural genomics, Nucleic + acid sites, features and motifs
  • Status: Up-to-date
  • Source: + https://genie.weizmann.ac.il/software/nucleo_exe.html
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: nucleosome_prediction
  • Date + of first commit of the suite: 2016-09-27
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction
  • Galaxy + wrapper version: 3.0
  • Conda id: nucleosome_prediction
  • Conda + version: 3.0
  • EDAM operation (no superclasses): Prediction + and recognition, Nucleosome position prediction, Sequence analysis
  • EDAM + topic (no superclasses): Structural genomics, Nucleic acid sites, features + and motifs
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 118
  • No. of tool + users (all time) (usegalaxy.eu): 863
  • Tool usage (5 years) + (usegalaxy.eu): 19
  • Tool usage (all time) (usegalaxy.eu): + 26
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 118
  • No. + of tool users (all time) - all main servers: 863
  • Tool usage + (5 years) - all main servers: 19
  • Tool usage (all time) + - all main servers: 26
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: nucleosome_prediction + - description_md: '
  • Galaxy tool ids: nugen_nudup
  • Description: + Marks/removes PCR introduced duplicate molecules based on the molecular tagging + technology used in NuGEN products.
  • bio.tool id: nudup
  • bio.tool + ids: nudup
  • biii: nan
  • bio.tool name: + NuDup
  • bio.tool description: Marks/removes duplicate molecules + based on the molecular tagging technology used in Tecan products.
  • EDAM + operation: Duplication detection
  • EDAM topic: Sequencing
  • Status: + Up-to-date
  • Source: https://github.com/tecangenomics/nudup
  • ToolShed + categories: SAM, Metagenomics, Sequence Analysis, Transcriptomics
  • ToolShed + id: nugen_nudup
  • Date of first commit of the suite: + 2016-11-18
  • Galaxy wrapper owner: iuc
  • Galaxy + wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup
  • Galaxy + wrapper version: 2.3.3
  • Conda id: nudup
  • Conda + version: 2.3.3
  • EDAM operation (no superclasses): + Duplication detection
  • EDAM topic (no superclasses): Sequencing
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: nugen_nudup + - description_md: '
  • Galaxy tool ids: obisindicators, obis_data
  • Description: + Compute biodiveristy indicators for marine data from obis
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/Marie59/obisindicators
  • ToolShed + categories: Ecology
  • ToolShed id: nan
  • Date + of first commit of the suite: 2022-11-04
  • Galaxy wrapper + owner: ecology
  • Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators
  • Galaxy + wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators
  • Galaxy + wrapper version: 0.0.2
  • Conda id: r-base
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 2
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 352
  • No. of tool users (all time) (usegalaxy.eu): 352
  • Tool + usage (5 years) (usegalaxy.eu): 42
  • Tool usage (all time) + (usegalaxy.eu): 42
  • No. of tool users (5 years) (usegalaxy.org): + 8
  • No. of tool users (all time) (usegalaxy.org): 8
  • Tool + usage (5 years) (usegalaxy.org): 6
  • Tool usage (all time) + (usegalaxy.org): 6
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 360
  • No. of tool users (all time) - all main + servers: 360
  • Tool usage (5 years) - all main servers: + 48
  • Tool usage (all time) - all main servers: 48
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: obisindicators + - description_md: '
  • Galaxy tool ids: obi_illumina_pairend, obi_ngsfilter, + obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, + obi_uniq
  • Description: OBITools is a set of programs developed + to simplify the manipulation of sequence files
  • bio.tool id: + obitools
  • bio.tool ids: obitools
  • biii: + nan
  • bio.tool name: OBITools
  • 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.
  • EDAM + operation: Sequence analysis, Sequence analysis
  • EDAM topic: + Sequence analysis, DNA, Sequencing
  • Status: Up-to-date
  • Source: + http://metabarcoding.org/obitools
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: obitools
  • Date + of first commit of the suite: 2017-03-23
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools
  • Galaxy + wrapper version: 1.2.13
  • Conda id: obitools
  • Conda + version: 1.2.13
  • EDAM operation (no superclasses): + Sequence analysis, Sequence analysis
  • EDAM topic (no superclasses): + Sequence analysis, DNA, Sequencing
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 10
  • Available + on UseGalaxy.eu: 10
  • Available on UseGalaxy.fr: 10
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 10
  • Tools available on UseGalaxy.eu: + 10
  • Tools available on UseGalaxy.fr: 10
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + 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.no: 10
  • Tools available on Viral + Variant Visualizer (VVV): 0
  • No. of tool users (5 years) + (usegalaxy.eu): 37598
  • No. of tool users (all time) (usegalaxy.eu): + 37598
  • Tool usage (5 years) (usegalaxy.eu): 1277
  • Tool + usage (all time) (usegalaxy.eu): 1277
  • No. of tool users + (5 years) (usegalaxy.org): 0
  • No. of tool users (all time) + (usegalaxy.org): 0
  • Tool usage (5 years) (usegalaxy.org): + 0
  • Tool usage (all time) (usegalaxy.org): 0
  • No. + of tool users (5 years) (usegalaxy.org.au): 3862
  • No. of + tool users (all time) (usegalaxy.org.au): 3862
  • Tool usage + (5 years) (usegalaxy.org.au): 280
  • Tool usage (all time) + (usegalaxy.org.au): 280
  • No. of tool users (5 years) - all + main servers: 41460
  • No. of tool users (all time) - all + main servers: 41460
  • Tool usage (5 years) - all main servers: + 1557
  • Tool usage (all time) - all main servers: 1557
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: obitools + - description_md: '
  • Galaxy tool ids: omark
  • Description: + Proteome quality assessment software
  • bio.tool id: omark
  • bio.tool + ids: omark
  • biii: nan
  • bio.tool name: + OMArk
  • bio.tool description: Proteome quality assessment + software
  • EDAM operation: Sequence assembly validation, + Differential protein expression profiling
  • EDAM topic: Proteomics, + Sequence analysis, Statistics and probability
  • Status: To + update
  • Source: https://github.com/DessimozLab/OMArk
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: omark
  • Date + of first commit of the suite: 2023-11-15
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark
  • Galaxy + wrapper version: 0.3.0
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): Sequence + assembly validation, Differential protein expression profiling
  • EDAM + topic (no superclasses): Proteomics, Sequence analysis, Statistics and + probability
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 158
  • No. of tool + users (all time) (usegalaxy.eu): 158
  • Tool usage (5 years) + (usegalaxy.eu): 12
  • Tool usage (all time) (usegalaxy.eu): + 12
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 158
  • No. + of tool users (all time) - all main servers: 158
  • Tool usage + (5 years) - all main servers: 12
  • Tool usage (all time) + - all main servers: 12
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: omark + - description_md: '
  • Galaxy tool ids: orfipy
  • Description: + Galaxy wrapper for ORFIPY
  • bio.tool id: orfipy
  • bio.tool + ids: orfipy
  • biii: nan
  • bio.tool name: + orfipy
  • 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.
  • EDAM + operation: Coding region prediction, Database search, Transcriptome assembly, + De-novo assembly
  • EDAM topic: Computer science, RNA-Seq, + Transcriptomics, Small molecules
  • Status: Up-to-date
  • Source: + https://github.com/urmi-21/orfipy
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: orfipy
  • Date + of first commit of the suite: 2022-04-07
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy
  • Galaxy + wrapper version: 0.0.4
  • Conda id: orfipy
  • Conda + version: 0.0.4
  • EDAM operation (no superclasses): + Coding region prediction, Database search, Transcriptome assembly, De-novo assembly
  • EDAM + topic (no superclasses): Computer science, RNA-Seq, Transcriptomics, + Small molecules
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 897
  • No. of tool + users (all time) (usegalaxy.eu): 897
  • Tool usage (5 years) + (usegalaxy.eu): 99
  • Tool usage (all time) (usegalaxy.eu): + 99
  • No. of tool users (5 years) (usegalaxy.org): 1792
  • No. + of tool users (all time) (usegalaxy.org): 1792
  • Tool usage + (5 years) (usegalaxy.org): 239
  • Tool usage (all time) (usegalaxy.org): + 239
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 2689
  • No. + of tool users (all time) - all main servers: 2689
  • Tool + usage (5 years) - all main servers: 338
  • Tool usage (all + time) - all main servers: 338
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: orfipy + - description_md: '
  • Galaxy tool ids: orthofinder_onlygroups
  • Description: + Accurate inference of orthologous gene groups made easy
  • bio.tool + id: OrthoFinder
  • bio.tool ids: OrthoFinder
  • biii: + nan
  • bio.tool name: OrthoFinder
  • 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.
  • EDAM + operation: Genome comparison, Phylogenetic tree generation (from molecular + sequences), Phylogenetic tree analysis, Genome alignment
  • EDAM + topic: Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, + Sequence analysis
  • Status: To update
  • Source: + https://github.com/davidemms/OrthoFinder
  • ToolShed categories: + Phylogenetics, Sequence Analysis
  • ToolShed id: orthofinder
  • Date + of first commit of the suite: 2017-08-30
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder
  • Galaxy + wrapper version: 2.5.5
  • Conda id: orthofinder
  • Conda + version: 3.0.1b1
  • EDAM operation (no superclasses): + Genome comparison, Genome alignment
  • EDAM topic (no superclasses): + Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 2018
  • No. of tool + users (all time) (usegalaxy.eu): 2018
  • Tool usage (5 years) + (usegalaxy.eu): 419
  • Tool usage (all time) (usegalaxy.eu): + 419
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 438
  • No. + of tool users (all time) (usegalaxy.org.au): 438
  • Tool usage + (5 years) (usegalaxy.org.au): 58
  • Tool usage (all time) + (usegalaxy.org.au): 58
  • No. of tool users (5 years) - all + main servers: 2456
  • No. of tool users (all time) - all main + servers: 2456
  • Tool usage (5 years) - all main servers: + 477
  • Tool usage (all time) - all main servers: 477
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: orthofinder + - description_md: '
  • Galaxy tool ids: fasta_cli, ident_params, + peptide_shaker, search_gui
  • Description: PeptideShaker and + SearchGUI
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + http://compomics.github.io
  • ToolShed categories: Proteomics
  • ToolShed + id: peptideshaker
  • Date of first commit of the suite: + 2021-04-02
  • Galaxy wrapper owner: galaxyp
  • Galaxy + wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker
  • Galaxy + wrapper version: nan
  • Conda id: searchgui
  • Conda + version: 4.3.11
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 4
  • Available on UseGalaxy.org.au: + 4
  • Available on UseGalaxy.eu: 4
  • Available + on UseGalaxy.fr: 4
  • Tools available on UseGalaxy.org (Main): + 4
  • Tools available on UseGalaxy.org.au: 4
  • Tools + available on UseGalaxy.eu: 4
  • Tools available on UseGalaxy.fr: + 4
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools 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: 4
  • Tools available on UseGalaxy.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 11986
  • No. of tool + users (all time) (usegalaxy.eu): 17898
  • Tool usage (5 years) + (usegalaxy.eu): 1046
  • Tool usage (all time) (usegalaxy.eu): + 1153
  • No. of tool users (5 years) (usegalaxy.org): 1314
  • No. + of tool users (all time) (usegalaxy.org): 1314
  • Tool usage + (5 years) (usegalaxy.org): 389
  • Tool usage (all time) (usegalaxy.org): + 389
  • No. of tool users (5 years) (usegalaxy.org.au): 3034
  • No. + of tool users (all time) (usegalaxy.org.au): 3034
  • Tool + usage (5 years) (usegalaxy.org.au): 118
  • Tool usage (all + time) (usegalaxy.org.au): 118
  • No. of tool users (5 years) + - all main servers: 16334
  • No. of tool users (all time) + - all main servers: 22246
  • Tool usage (5 years) - all main + servers: 1553
  • Tool usage (all time) - all main servers: + 1660
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: peptideshaker + - description_md: '
  • Galaxy tool ids: pfamscan
  • Description: + Search a FASTA sequence against a library of Pfam HMM.
  • bio.tool + id: pfamscan
  • bio.tool ids: pfamscan
  • biii: + nan
  • bio.tool name: PfamScan
  • bio.tool description: + This tool is used to search a FASTA sequence against a library of Pfam HMM.
  • EDAM + operation: Protein sequence analysis
  • EDAM topic: + Sequence analysis
  • Status: Up-to-date
  • Source: + http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: pfamscan
  • Date + of first commit of the suite: 2023-02-02
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan
  • Galaxy + wrapper version: 1.6
  • Conda id: pfam_scan
  • Conda + version: 1.6
  • EDAM operation (no superclasses): Protein + sequence analysis
  • EDAM topic (no superclasses): Sequence + analysis
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 773
  • No. of tool + users (all time) (usegalaxy.eu): 773
  • Tool usage (5 years) + (usegalaxy.eu): 60
  • Tool usage (all time) (usegalaxy.eu): + 60
  • No. of tool users (5 years) (usegalaxy.org): 495
  • No. + of tool users (all time) (usegalaxy.org): 495
  • Tool usage + (5 years) (usegalaxy.org): 72
  • Tool usage (all time) (usegalaxy.org): + 72
  • No. of tool users (5 years) (usegalaxy.org.au): 246
  • No. + of tool users (all time) (usegalaxy.org.au): 246
  • Tool usage + (5 years) (usegalaxy.org.au): 17
  • Tool usage (all time) + (usegalaxy.org.au): 17
  • No. of tool users (5 years) - all + main servers: 1514
  • No. of tool users (all time) - all main + servers: 1514
  • Tool usage (5 years) - all main servers: + 149
  • Tool usage (all time) - all main servers: 149
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: pfamscan + - description_md: "
  • Galaxy tool ids: pharokka
  • Description:\ + \ rapid standardised annotation tool for bacteriophage genomes and metagenomes
  • bio.tool\ + \ id: pharokka
  • bio.tool ids: pharokka
  • biii:\ + \ nan
  • bio.tool name: Pharokka
  • bio.tool description:\ + \ Pharokka is a rapid standardised annotation tool for bacteriophage genomes\ + \ and metagenomes.
  • EDAM operation: 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
  • Status: To\ + \ update
  • Source: https://github.com/gbouras13/pharokka
  • ToolShed\ + \ categories: Genome annotation
  • ToolShed id: pharokka
  • Date\ + \ of first commit of the suite: 2023-02-14
  • Galaxy wrapper\ + \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
  • Galaxy\ + \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
  • Galaxy\ + \ wrapper version: 1.3.2
  • Conda id: \n \ + \ pharokka\n
  • Conda version: nan
  • EDAM\ + \ operation (no superclasses): Genome annotation, Antimicrobial resistance\ + \ prediction, tRNA gene prediction, Formatting, Sequence assembly
  • EDAM\ + \ topic (no superclasses): Metagenomics, Sequence sites, features and\ + \ motifs, Workflows, Functional, regulatory and non-coding RNA
  • Available\ + \ on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au:\ + \ 1
  • Available on UseGalaxy.eu: 1
  • Available\ + \ on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main):\ + \ 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools\ + \ available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr:\ + \ 0
  • Tools available on APOSTL: 0
  • Tools available\ + \ on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools\ + \ available on ChemFlow: 0
  • Tools available on Coloc-stats:\ + \ 0
  • Tools available on CropGalaxy: 0
  • Tools\ + \ available 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.no:\ + \ 0
  • Tools available on Viral Variant Visualizer (VVV):\ + \ 0
  • No. of tool users (5 years) (usegalaxy.eu): 5462
  • No.\ + \ of tool users (all time) (usegalaxy.eu): 5462
  • Tool usage\ + \ (5 years) (usegalaxy.eu): 334
  • Tool usage (all time) (usegalaxy.eu):\ + \ 334
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No.\ + \ of tool users (all time) (usegalaxy.org): 0
  • Tool usage\ + \ (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org):\ + \ 0
  • No. of tool users (5 years) (usegalaxy.org.au): 309
  • No.\ + \ of tool users (all time) (usegalaxy.org.au): 309
  • Tool\ + \ usage (5 years) (usegalaxy.org.au): 52
  • Tool usage (all\ + \ time) (usegalaxy.org.au): 52
  • No. of tool users (5 years)\ + \ - all main servers: 5771
  • No. of tool users (all time)\ + \ - all main servers: 5771
  • Tool usage (5 years) - all main\ + \ servers: 386
  • Tool usage (all time) - all main servers:\ + \ 386
  • Reviewed: True
  • To keep: True
  • Deprecated:\ + \ False
" + title_md: pharokka + - description_md: '
  • Galaxy tool ids: phyloseq_from_biom, phyloseq_from_dada2, + phyloseq_plot_ordination, phyloseq_plot_richness
  • Description: + Handling and analysis of high-throughput microbiome census data
  • bio.tool + id: phyloseq
  • bio.tool ids: phyloseq
  • biii: + nan
  • bio.tool name: phyloseq
  • bio.tool description: + Provides a set of classes and tools to facilitate the import, storage, analysis, + and graphical display of microbiome census data.
  • EDAM operation: + Deposition, Analysis, Visualisation
  • EDAM topic: Microbiology, + Sequence analysis, Metagenomics
  • Status: Up-to-date
  • Source: + https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html
  • ToolShed + categories: Metagenomics
  • ToolShed id: phyloseq
  • Date + of first commit of the suite: 2022-03-03
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq
  • Galaxy + wrapper version: 1.46.0
  • Conda id: bioconductor-phyloseq
  • Conda + version: 1.46.0
  • EDAM operation (no superclasses): + Deposition, Analysis, Visualisation
  • EDAM topic (no superclasses): + Microbiology, Sequence analysis, Metagenomics
  • Available on UseGalaxy.org + (Main): 4
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 4
  • Available on UseGalaxy.fr: 4
  • Tools + available on UseGalaxy.org (Main): 4
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 4
  • Tools available on UseGalaxy.fr: 4
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1199
  • No. of tool users (all time) (usegalaxy.eu): 1199
  • Tool + usage (5 years) (usegalaxy.eu): 193
  • Tool usage (all time) + (usegalaxy.eu): 193
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 6
  • No. of tool users (all time) (usegalaxy.org.au): 6
  • Tool + usage (5 years) (usegalaxy.org.au): 1
  • Tool usage (all time) + (usegalaxy.org.au): 1
  • No. of tool users (5 years) - all + main servers: 1205
  • No. of tool users (all time) - all main + servers: 1205
  • Tool usage (5 years) - all main servers: + 194
  • Tool usage (all time) - all main servers: 194
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: phyloseq + - description_md: '
  • Galaxy tool ids: phyml
  • Description: + PhyML is a phylogeny software based on the maximum-likelihood principle.
  • bio.tool + id: phyml
  • bio.tool ids: phyml
  • biii: + nan
  • bio.tool name: PhyML
  • bio.tool description: + Phylogenetic estimation software using Maximum Likelihood
  • EDAM + operation: Phylogenetic tree generation (maximum likelihood and Bayesian + methods)
  • EDAM topic: Phylogenetics, Bioinformatics, Phylogenetics
  • Status: + Up-to-date
  • Source: http://www.atgc-montpellier.fr/phyml/
  • ToolShed + categories: Phylogenetics
  • ToolShed id: phyml
  • Date + of first commit of the suite: 2019-05-27
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml
  • Galaxy + wrapper version: 3.3.20220408
  • Conda id: phyml
  • Conda + version: 3.3.20220408
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): Phylogenetics, Bioinformatics, + Phylogenetics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1975
  • No. of tool + users (all time) (usegalaxy.eu): 2034
  • Tool usage (5 years) + (usegalaxy.eu): 246
  • Tool usage (all time) (usegalaxy.eu): + 258
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 553
  • No. + of tool users (all time) (usegalaxy.org.au): 564
  • Tool usage + (5 years) (usegalaxy.org.au): 140
  • Tool usage (all time) + (usegalaxy.org.au): 144
  • No. of tool users (5 years) - all + main servers: 2528
  • No. of tool users (all time) - all main + servers: 2598
  • Tool usage (5 years) - all main servers: + 386
  • Tool usage (all time) - all main servers: 402
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: phyml + - description_md: '
  • 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
  • Description: PICRUSt wrappers
  • bio.tool + id: picrust
  • bio.tool ids: picrust
  • biii: + nan
  • bio.tool name: PICRUSt
  • 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.
  • EDAM + operation: Phylogenetic reconstruction, Expression analysis, Genome annotation, + DNA barcoding
  • EDAM topic: Metagenomics, Microbial ecology, + Functional, regulatory and non-coding RNA, Metagenomic sequencing
  • Status: + To update
  • Source: https://picrust.github.io/picrust/
  • ToolShed + categories: Metagenomics
  • ToolShed id: picrust
  • Date + of first commit of the suite: 2017-07-31
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust
  • Galaxy + wrapper version: 1.1.1
  • Conda id: picrust
  • Conda + version: 1.1.4
  • EDAM operation (no superclasses): + Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding
  • EDAM + topic (no superclasses): Metagenomics, Microbial ecology, Functional, + regulatory and non-coding RNA, Metagenomic sequencing
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 6
  • Available on UseGalaxy.eu: 5
  • Available + on UseGalaxy.fr: 6
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 6
  • Tools + available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: + 6
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 5
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 867
  • No. of tool + users (all time) (usegalaxy.eu): 1128
  • Tool usage (5 years) + (usegalaxy.eu): 144
  • Tool usage (all time) (usegalaxy.eu): + 165
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 2106
  • No. + of tool users (all time) (usegalaxy.org.au): 2106
  • Tool + usage (5 years) (usegalaxy.org.au): 121
  • Tool usage (all + time) (usegalaxy.org.au): 121
  • No. of tool users (5 years) + - all main servers: 2973
  • No. of tool users (all time) - + all main servers: 3234
  • Tool usage (5 years) - all main + servers: 265
  • Tool usage (all time) - all main servers: + 286
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: picrust + - description_md: '
  • Galaxy tool ids: picrust2_add_descriptions, + picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, + picrust2_place_seqs, picrust2_shuffle_predictions
  • Description: + PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved + States
  • bio.tool id: picrust2
  • bio.tool ids: + picrust2
  • biii: nan
  • bio.tool name: + PICRUSt2
  • 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.
  • EDAM + operation: Phylogenetic reconstruction, Expression analysis, Rarefaction, + Pathway analysis
  • EDAM topic: Metagenomics, Microbiology, + Phylogenetics, Metagenomic sequencing
  • Status: Up-to-date
  • Source: + https://github.com/picrust/picrust2/wiki
  • ToolShed categories: + Metagenomics
  • ToolShed id: picrust2
  • Date of + first commit of the suite: 2021-11-07
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/picrust/picrust2
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2
  • Galaxy + wrapper version: 2.5.3
  • Conda id: picrust2
  • Conda + version: 2.5.3
  • EDAM operation (no superclasses): + Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis
  • EDAM + topic (no superclasses): Metagenomics, Microbiology, Phylogenetics, Metagenomic + sequencing
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 7
  • Available on UseGalaxy.eu: + 7
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 7
  • Tools available on UseGalaxy.eu: 7
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 2532
  • No. of tool + users (all time) (usegalaxy.eu): 2532
  • Tool usage (5 years) + (usegalaxy.eu): 382
  • Tool usage (all time) (usegalaxy.eu): + 382
  • No. of tool users (5 years) (usegalaxy.org): 1
  • No. + of tool users (all time) (usegalaxy.org): 1
  • Tool usage + (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): + 1
  • No. of tool users (5 years) (usegalaxy.org.au): 1311
  • No. + of tool users (all time) (usegalaxy.org.au): 1311
  • Tool + usage (5 years) (usegalaxy.org.au): 83
  • Tool usage (all + time) (usegalaxy.org.au): 83
  • No. of tool users (5 years) + - all main servers: 3844
  • No. of tool users (all time) - + all main servers: 3844
  • Tool usage (5 years) - all main + servers: 466
  • Tool usage (all time) - all main servers: + 466
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: picrust2 + - description_md: '
  • Galaxy tool ids: PlasFlow
  • Description: + PlasFlow - Prediction of plasmid sequences in metagenomic contigs.
  • bio.tool + id: plasflow
  • bio.tool ids: plasflow
  • biii: + nan
  • bio.tool name: PlasFlow
  • bio.tool description: + PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic + contigs.
  • EDAM operation: Sequence analysis
  • EDAM + topic: Metagenomics
  • Status: Up-to-date
  • Source: + https://github.com/smaegol/PlasFlow
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: plasflow
  • Date + of first commit of the suite: 2018-09-05
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow
  • Galaxy + wrapper version: 1.1.0
  • Conda id: plasflow
  • Conda + version: 1.1.0
  • EDAM operation (no superclasses): + Sequence analysis
  • EDAM topic (no superclasses): Metagenomics
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 37086
  • No. of tool + users (all time) (usegalaxy.eu): 37272
  • Tool usage (5 years) + (usegalaxy.eu): 711
  • Tool usage (all time) (usegalaxy.eu): + 734
  • No. of tool users (5 years) (usegalaxy.org): 6346
  • No. + of tool users (all time) (usegalaxy.org): 6346
  • Tool usage + (5 years) (usegalaxy.org): 583
  • Tool usage (all time) (usegalaxy.org): + 583
  • No. of tool users (5 years) (usegalaxy.org.au): 3065
  • No. + of tool users (all time) (usegalaxy.org.au): 3065
  • Tool + usage (5 years) (usegalaxy.org.au): 61
  • Tool usage (all + time) (usegalaxy.org.au): 61
  • No. of tool users (5 years) + - all main servers: 46497
  • No. of tool users (all time) + - all main servers: 46683
  • Tool usage (5 years) - all main + servers: 1355
  • Tool usage (all time) - all main servers: + 1378
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: plasflow + - description_md: '
  • Galaxy tool ids: plasmidfinder
  • 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"
  • bio.tool + id: PlasmidFinder
  • bio.tool ids: PlasmidFinder
  • biii: + nan
  • bio.tool name: PlasmidFinder
  • bio.tool + description: PlasmidFinder is a tool for the identification and typing + of Plasmid Replicons in Whole-Genome Sequencing (WGS).
  • EDAM operation: + Genome assembly, Scaffolding, Multilocus sequence typing
  • EDAM + topic: Whole genome sequencing, Sequence assembly, Mapping, Probes and + primers
  • Status: Up-to-date
  • Source: + https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: plasmidfinder
  • Date + of first commit of the suite: 2022-09-19
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder
  • Galaxy + wrapper version: 2.1.6
  • Conda id: plasmidfinder
  • Conda + version: 2.1.6
  • EDAM operation (no superclasses): + Genome assembly, Scaffolding, Multilocus sequence typing
  • EDAM + topic (no superclasses): Whole genome sequencing, Sequence assembly, + Mapping, Probes and primers
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 14652
  • No. of tool users (all time) (usegalaxy.eu): 14652
  • Tool + usage (5 years) (usegalaxy.eu): 251
  • Tool usage (all time) + (usegalaxy.eu): 251
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 101
  • No. of tool users (all time) (usegalaxy.org.au): 101
  • Tool + usage (5 years) (usegalaxy.org.au): 18
  • Tool usage (all + time) (usegalaxy.org.au): 18
  • No. of tool users (5 years) + - all main servers: 14753
  • No. of tool users (all time) + - all main servers: 14753
  • Tool usage (5 years) - all main + servers: 269
  • Tool usage (all time) - all main servers: + 269
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: plasmidfinder + - description_md: '
  • Galaxy tool ids: plasmidspades
  • Description: + Genome assembler for assemblying plasmid
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + nan
  • ToolShed categories: Assembly
  • ToolShed + id: plasmidspades
  • Date of first commit of the suite: + 2016-06-06
  • Galaxy wrapper owner: nml
  • Galaxy + wrapper source: nan
  • Galaxy wrapper parsed folder: + https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades
  • Galaxy + wrapper version: 1.1
  • Conda id: spades
  • Conda + version: 4.0.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available 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: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: plasmidspades + - description_md: '
  • Galaxy tool ids: polypolish
  • 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."
  • bio.tool id: + Polypolish
  • bio.tool ids: Polypolish
  • biii: + nan
  • bio.tool name: Polypolish
  • 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.
  • EDAM operation: Genome assembly, Read mapping, + Mapping assembly, Sequencing error detection
  • EDAM topic: + Sequence assembly, Sequence composition, complexity and repeats, Mapping
  • Status: + To update
  • Source: https://github.com/rrwick/Polypolish
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: polypolish
  • Date + of first commit of the suite: 2022-09-22
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish
  • Galaxy + wrapper version: 0.5.0
  • Conda id: polypolish
  • Conda + version: 0.6.0
  • EDAM operation (no superclasses): + Genome assembly, Read mapping, Mapping assembly, Sequencing error detection
  • EDAM + topic (no superclasses): Sequence assembly, Sequence composition, complexity + and repeats, Mapping
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 731
  • No. of tool users (all time) (usegalaxy.eu): 731
  • Tool + usage (5 years) (usegalaxy.eu): 86
  • Tool usage (all time) + (usegalaxy.eu): 86
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 42
  • No. of tool users (all time) (usegalaxy.org.au): 42
  • Tool + usage (5 years) (usegalaxy.org.au): 4
  • Tool usage (all time) + (usegalaxy.org.au): 4
  • No. of tool users (5 years) - all + main servers: 773
  • No. of tool users (all time) - all main + servers: 773
  • Tool usage (5 years) - all main servers: + 90
  • Tool usage (all time) - all main servers: 90
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: polypolish + - description_md: '
  • Galaxy tool ids: prodigal
  • Description: + A protein-coding gene prediction software tool for bacterial and archaeal genomes
  • bio.tool + id: prodigal
  • bio.tool ids: prodigal
  • biii: + nan
  • bio.tool name: Prodigal
  • bio.tool description: + Fast, reliable protein-coding gene prediction for prokaryotic genomes.
  • EDAM + operation: Genome annotation
  • EDAM topic: Genomics, + Sequence analysis
  • Status: Up-to-date
  • Source: + https://github.com/hyattpd/Prodigal
  • ToolShed categories: + Genome annotation
  • ToolShed id: prodigal
  • Date + of first commit of the suite: 2024-03-14
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal
  • Galaxy + wrapper version: 2.6.3
  • Conda id: prodigal
  • Conda + version: 2.6.3
  • EDAM operation (no superclasses): + Genome annotation
  • EDAM topic (no superclasses): Genomics, + Sequence analysis
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1902
  • No. of tool + users (all time) (usegalaxy.eu): 1902
  • Tool usage (5 years) + (usegalaxy.eu): 167
  • Tool usage (all time) (usegalaxy.eu): + 167
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1902
  • No. + of tool users (all time) - all main servers: 1902
  • Tool + usage (5 years) - all main servers: 167
  • Tool usage (all + time) - all main servers: 167
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: prodigal + - description_md: '
  • Galaxy tool ids: prokka
  • Description: + Rapid annotation of prokaryotic genomes
  • bio.tool id: prokka
  • bio.tool + ids: prokka
  • biii: nan
  • bio.tool name: + Prokka
  • bio.tool description: Software tool to annotate + bacterial, archaeal and viral genomes quickly and produce standards-compliant + output files.
  • EDAM operation: Gene prediction, Coding region + prediction, Genome annotation
  • EDAM topic: Genomics, Model + organisms, Virology
  • Status: Up-to-date
  • Source: + http://github.com/tseemann/prokka
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: prokka
  • Date + of first commit of the suite: 2016-10-10
  • Galaxy wrapper + owner: crs4
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka
  • Galaxy + wrapper version: 1.14.6
  • Conda id: prokka
  • Conda + version: 1.14.6
  • EDAM operation (no superclasses): + Coding region prediction, Genome annotation
  • EDAM topic (no superclasses): + Genomics, Model organisms, Virology
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 464359
  • No. of tool users (all time) (usegalaxy.eu): 476554
  • Tool + usage (5 years) (usegalaxy.eu): 7475
  • Tool usage (all time) + (usegalaxy.eu): 7721
  • No. of tool users (5 years) (usegalaxy.org): + 313285
  • No. of tool users (all time) (usegalaxy.org): 331256
  • Tool + usage (5 years) (usegalaxy.org): 11243
  • Tool usage (all + time) (usegalaxy.org): 12384
  • No. of tool users (5 years) + (usegalaxy.org.au): 131211
  • No. of tool users (all time) + (usegalaxy.org.au): 141875
  • Tool usage (5 years) (usegalaxy.org.au): + 4358
  • Tool usage (all time) (usegalaxy.org.au): 4947
  • No. + of tool users (5 years) - all main servers: 908855
  • No. + of tool users (all time) - all main servers: 949685
  • Tool + usage (5 years) - all main servers: 23076
  • Tool usage (all + time) - all main servers: 25052
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: prokka + - description_md: '
  • Galaxy tool ids: promer4_substitutions
  • Description: + Aligns two sets of contigs and reports amino acid substitutions between them
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/phac-nml/promer
  • ToolShed + categories: Assembly
  • ToolShed id: promer
  • Date + of first commit of the suite: 2019-12-14
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/promer
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer
  • Galaxy + wrapper version: 1.2
  • Conda id: python
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: promer + - description_md: '
  • Galaxy tool ids: proteinortho, proteinortho_grab_proteins, + proteinortho_summary
  • Description: Proteinortho is a tool + to detect orthologous proteins/genes within different species.
  • bio.tool + id: proteinortho
  • bio.tool ids: proteinortho
  • biii: + nan
  • bio.tool name: Proteinortho
  • bio.tool + description: Proteinortho is a tool to detect orthologous genes within + different species
  • EDAM operation: Sequence clustering, + Sequence analysis
  • EDAM topic: Comparative genomics
  • Status: + To update
  • Source: https://gitlab.com/paulklemm_PHD/proteinortho
  • ToolShed + categories: Proteomics
  • ToolShed id: proteinortho
  • Date + of first commit of the suite: 2020-10-02
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://gitlab.com/paulklemm_PHD/proteinortho
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho
  • Galaxy + wrapper version: 6.3.1
  • Conda id: proteinortho
  • Conda + version: 6.3.2
  • EDAM operation (no superclasses): + Sequence clustering, Sequence analysis
  • EDAM topic (no superclasses): + Comparative genomics
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 3
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 3
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 3962
  • No. of tool users (all time) (usegalaxy.eu): 3962
  • Tool + usage (5 years) (usegalaxy.eu): 501
  • Tool usage (all time) + (usegalaxy.eu): 501
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 3962
  • No. of tool users (all time) - all main + servers: 3962
  • Tool usage (5 years) - all main servers: + 501
  • Tool usage (all time) - all main servers: 501
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: proteinortho + - description_md: '
  • Galaxy tool ids: pycoqc
  • Description: + QC metrics for ONT Basecalling
  • bio.tool id: pycoqc
  • bio.tool + ids: pycoqc
  • biii: nan
  • bio.tool name: + pycoQC
  • bio.tool description: PycoQC computes metrics and + generates interactive QC plots for Oxford Nanopore technologies sequencing data.
  • EDAM + operation: Sequencing quality control, Statistical calculation
  • EDAM + topic: Sequence analysis, Data quality management, Sequencing
  • Status: + Up-to-date
  • Source: https://github.com/tleonardi/pycoQC
  • ToolShed + categories: Nanopore
  • ToolShed id: pycoqc
  • Date + of first commit of the suite: 2021-03-02
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc
  • Galaxy + wrapper version: 2.5.2
  • Conda id: pycoqc
  • Conda + version: 2.5.2
  • EDAM operation (no superclasses): + Sequencing quality control, Statistical calculation
  • EDAM topic + (no superclasses): Sequence analysis, Data quality management, Sequencing
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 22742
  • No. of tool + users (all time) (usegalaxy.eu): 22742
  • Tool usage (5 years) + (usegalaxy.eu): 557
  • Tool usage (all time) (usegalaxy.eu): + 557
  • No. of tool users (5 years) (usegalaxy.org): 2159
  • No. + of tool users (all time) (usegalaxy.org): 2159
  • Tool usage + (5 years) (usegalaxy.org): 716
  • Tool usage (all time) (usegalaxy.org): + 716
  • No. of tool users (5 years) (usegalaxy.org.au): 776
  • No. + of tool users (all time) (usegalaxy.org.au): 776
  • Tool usage + (5 years) (usegalaxy.org.au): 448
  • Tool usage (all time) + (usegalaxy.org.au): 448
  • No. of tool users (5 years) - all + main servers: 25677
  • No. of tool users (all time) - all + main servers: 25677
  • Tool usage (5 years) - all main servers: + 1721
  • Tool usage (all time) - all main servers: 1721
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: pycoqc + - description_md: '
  • Galaxy tool ids: pygenomeTracks
  • Description: + pyGenomeTracks: Standalone program and library to plot beautiful genome browser + tracks.
  • bio.tool id: pygenometracks
  • bio.tool + ids: pygenometracks
  • biii: nan
  • bio.tool + name: pyGenomeTracks
  • 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:.
  • EDAM operation: Visualisation, Formatting
  • EDAM + topic: Model organisms, Imaging, Workflows
  • Status: + To update
  • Source: https://github.com/deeptools/pyGenomeTracks
  • ToolShed + categories: Visualization
  • ToolShed id: pygenometracks
  • Date + of first commit of the suite: 2020-03-27
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks
  • Galaxy + wrapper version: 3.8
  • Conda id: pygenometracks
  • Conda + version: 3.9
  • EDAM operation (no superclasses): Visualisation, + Formatting
  • EDAM topic (no superclasses): Model organisms, + Imaging, Workflows
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 12858
  • No. of tool + users (all time) (usegalaxy.eu): 13232
  • Tool usage (5 years) + (usegalaxy.eu): 986
  • Tool usage (all time) (usegalaxy.eu): + 996
  • No. of tool users (5 years) (usegalaxy.org): 8092
  • No. + of tool users (all time) (usegalaxy.org): 8092
  • Tool usage + (5 years) (usegalaxy.org): 943
  • Tool usage (all time) (usegalaxy.org): + 943
  • No. of tool users (5 years) (usegalaxy.org.au): 3238
  • No. + of tool users (all time) (usegalaxy.org.au): 3238
  • Tool + usage (5 years) (usegalaxy.org.au): 124
  • Tool usage (all + time) (usegalaxy.org.au): 124
  • No. of tool users (5 years) + - all main servers: 24188
  • No. of tool users (all time) + - all main servers: 24562
  • Tool usage (5 years) - all main + servers: 2053
  • Tool usage (all time) - all main servers: + 2063
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: pygenometracks + - description_md: '
  • Galaxy tool ids: qiime_collapse_samples, + qiime_make_otu_table
  • Description: QIIME to perform microbial + community analysis
  • bio.tool id: qiime_add_on
  • bio.tool + ids: qiime_core, qiime_add_on
  • biii: nan
  • bio.tool + name: qiime_add_on
  • bio.tool description: QIIME 2 + is a next-generation microbiome bioinformatics platform that is extensible, + free, open source, and community developed.
  • EDAM operation: + Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, + Sequencing quality control
  • EDAM topic: Microbial ecology, + Phylogeny, Metagenomics, Metatranscriptomics
  • Status: To + update
  • Source: http://www.qiime.org
  • ToolShed + categories: Metagenomics
  • ToolShed id: qiime
  • Date + of first commit of the suite: 2017-01-25
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on
  • Galaxy + wrapper version: nan
  • Conda id: qiime
  • Conda + version: 1.9.1
  • EDAM operation (no superclasses): + Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, + Sequencing quality control
  • EDAM topic (no superclasses): + Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 2
  • Available + on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: + 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 2092
  • No. of tool + users (all time) (usegalaxy.eu): 2342
  • Tool usage (5 years) + (usegalaxy.eu): 209
  • Tool usage (all time) (usegalaxy.eu): + 238
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 2
  • No. + of tool users (all time) (usegalaxy.org.au): 2
  • Tool usage + (5 years) (usegalaxy.org.au): 1
  • Tool usage (all time) (usegalaxy.org.au): + 1
  • No. of tool users (5 years) - all main servers: 2094
  • No. + of tool users (all time) - all main servers: 2344
  • Tool + usage (5 years) - all main servers: 210
  • Tool usage (all + time) - all main servers: 239
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: qiime_add_on + - description_md: "
  • 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
  • Description:\ + \ QIIME to perform microbial community analysis
  • bio.tool id:\ + \ qiime_core
  • bio.tool ids: qiime_core
  • biii:\ + \ nan
  • bio.tool name: qiime_core
  • bio.tool\ + \ description: QIIME 2\u2122 is a next-generation microbiome bioinformatics\ + \ platform that is extensible, free, open source, and community developed.
  • EDAM\ + \ operation: Demultiplexing, Visualisation, Taxonomic classification,\ + \ Phylogenetic analysis, Sequencing quality control
  • EDAM topic:\ + \ Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics
  • Status:\ + \ To update
  • Source: http://www.qiime.org
  • ToolShed\ + \ categories: Metagenomics
  • ToolShed id: qiime
  • Date\ + \ of first commit of the suite: 2017-06-14
  • Galaxy wrapper\ + \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
  • Galaxy\ + \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core
  • Galaxy\ + \ wrapper version: nan
  • Conda id: qiime
  • Conda\ + \ version: 1.9.1
  • EDAM operation (no superclasses):\ + \ Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis,\ + \ Sequencing quality control
  • EDAM topic (no superclasses):\ + \ Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics
  • Available\ + \ on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au:\ + \ 0
  • Available on UseGalaxy.eu: 32
  • Available\ + \ on UseGalaxy.fr: 32
  • Tools available on UseGalaxy.org\ + \ (Main): 0
  • Tools available on UseGalaxy.org.au:\ + \ 0
  • Tools available on UseGalaxy.eu: 32
  • Tools\ + \ available on UseGalaxy.fr: 32
  • Tools available on APOSTL:\ + \ 0
  • Tools available on ARGs-OAP: 0
  • Tools\ + \ available on CIRM-CFBP: 0
  • Tools available on ChemFlow:\ + \ 0
  • Tools available 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.no: 31
  • Tools\ + \ available on Viral Variant Visualizer (VVV): 0
  • No. of\ + \ tool users (5 years) (usegalaxy.eu): 31825
  • No. of tool\ + \ users (all time) (usegalaxy.eu): 34677
  • Tool usage (5\ + \ years) (usegalaxy.eu): 3375
  • Tool usage (all time) (usegalaxy.eu):\ + \ 3785
  • No. of tool users (5 years) (usegalaxy.org): 1
  • No.\ + \ of tool users (all time) (usegalaxy.org): 1
  • Tool usage\ + \ (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org):\ + \ 1
  • No. of tool users (5 years) (usegalaxy.org.au): 14
  • No.\ + \ of tool users (all time) (usegalaxy.org.au): 14
  • Tool\ + \ usage (5 years) (usegalaxy.org.au): 4
  • Tool usage (all\ + \ time) (usegalaxy.org.au): 4
  • No. of tool users (5 years)\ + \ - all main servers: 31840
  • No. of tool users (all time)\ + \ - all main servers: 34692
  • Tool usage (5 years) - all\ + \ main servers: 3380
  • Tool usage (all time) - all main servers:\ + \ 3790
  • Reviewed: True
  • To keep: True
  • Deprecated:\ + \ False
" + title_md: qiime_core + - description_md: '
  • Galaxy tool ids: qualimap_bamqc, qualimap_counts, + qualimap_multi_bamqc, qualimap_rnaseq
  • 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.
  • bio.tool id: qualimap
  • bio.tool ids: + qualimap
  • biii: nan
  • bio.tool name: + QualiMap
  • 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.
  • EDAM operation: Sequencing quality control
  • EDAM + topic: Data quality management
  • Status: Up-to-date
  • Source: + http://qualimap.bioinfo.cipf.es/
  • ToolShed categories: Sequence + Analysis, Transcriptomics, SAM
  • ToolShed id: qualimap
  • Date + of first commit of the suite: 2019-10-10
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap
  • Galaxy + wrapper version: 2.3
  • Conda id: qualimap
  • Conda + version: 2.3
  • EDAM operation (no superclasses): Sequencing + quality control
  • EDAM topic (no superclasses): Data quality + management
  • Available on UseGalaxy.org (Main): 4
  • Available + on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: + 4
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: + 4
  • Tools available on UseGalaxy.eu: 4
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 4
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 684820
  • No. of tool + users (all time) (usegalaxy.eu): 684820
  • Tool usage (5 years) + (usegalaxy.eu): 3239
  • Tool usage (all time) (usegalaxy.eu): + 3239
  • No. of tool users (5 years) (usegalaxy.org): 90503
  • No. + of tool users (all time) (usegalaxy.org): 90503
  • Tool usage + (5 years) (usegalaxy.org): 3881
  • Tool usage (all time) (usegalaxy.org): + 3881
  • No. of tool users (5 years) (usegalaxy.org.au): 29018
  • No. + of tool users (all time) (usegalaxy.org.au): 29018
  • Tool + usage (5 years) (usegalaxy.org.au): 826
  • Tool usage (all + time) (usegalaxy.org.au): 826
  • No. of tool users (5 years) + - all main servers: 804341
  • No. of tool users (all time) + - all main servers: 804341
  • Tool usage (5 years) - all main + servers: 7946
  • Tool usage (all time) - all main servers: + 7946
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: qualimap + - description_md: '
  • Galaxy tool ids: quast
  • Description: + Quast (Quality ASsessment Tool) evaluates genome assemblies.
  • bio.tool + id: quast
  • bio.tool ids: quast
  • biii: + nan
  • bio.tool name: QUAST
  • bio.tool description: + QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome + assemblies by computing various metrics and providing nice reports.
  • EDAM + operation: Visualisation, Sequence assembly validation
  • EDAM + topic: Sequence assembly
  • Status: Up-to-date
  • Source: + http://quast.bioinf.spbau.ru/
  • ToolShed categories: Assembly
  • ToolShed + id: quast
  • Date of first commit of the suite: 2018-02-10
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast
  • Galaxy + wrapper version: 5.2.0
  • Conda id: quast
  • Conda + version: 5.2.0
  • EDAM operation (no superclasses): + Visualisation, Sequence assembly validation
  • EDAM topic (no superclasses): + Sequence assembly
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 67737
  • No. of tool + users (all time) (usegalaxy.eu): 69738
  • Tool usage (5 years) + (usegalaxy.eu): 7787
  • Tool usage (all time) (usegalaxy.eu): + 7971
  • No. of tool users (5 years) (usegalaxy.org): 51925
  • No. + of tool users (all time) (usegalaxy.org): 56602
  • Tool usage + (5 years) (usegalaxy.org): 9692
  • Tool usage (all time) (usegalaxy.org): + 10646
  • No. of tool users (5 years) (usegalaxy.org.au): 32003
  • No. + of tool users (all time) (usegalaxy.org.au): 34145
  • Tool + usage (5 years) (usegalaxy.org.au): 3890
  • Tool usage (all + time) (usegalaxy.org.au): 4127
  • No. of tool users (5 years) + - all main servers: 151665
  • No. of tool users (all time) + - all main servers: 160485
  • Tool usage (5 years) - all main + servers: 21369
  • Tool usage (all time) - all main servers: + 22744
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: quast + - description_md: '
  • Galaxy tool ids: quickmerge
  • Description: + Merge long-read and hybrid assemblies to increase contiguity
  • bio.tool + id: quickmerge
  • bio.tool ids: quickmerge
  • biii: + nan
  • bio.tool name: quickmerge
  • 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.
  • EDAM + operation: Genome assembly, Scaffolding, De-novo assembly, Genotyping
  • EDAM + topic: Structural variation, Sequence assembly, DNA polymorphism, Whole + genome sequencing, Genotype and phenotype
  • Status: Up-to-date
  • Source: + https://github.com/mahulchak/quickmerge
  • ToolShed categories: + Assembly
  • ToolShed id: quickmerge
  • Date of + first commit of the suite: 2022-07-08
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge
  • Galaxy + wrapper version: 0.3
  • Conda id: quickmerge
  • Conda + version: 0.3
  • EDAM operation (no superclasses): Genome + assembly, Scaffolding, De-novo assembly, Genotyping
  • EDAM topic + (no superclasses): Structural variation, Sequence assembly, DNA polymorphism, + Whole genome sequencing, Genotype and phenotype
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: quickmerge + - description_md: '
  • Galaxy tool ids: meta_rna
  • Description: + Identification of ribosomal RNA genes in metagenomic fragments.
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: http://weizhong-lab.ucsd.edu/meta_rna/
  • ToolShed + categories: RNA
  • ToolShed id: rrna
  • Date + of first commit of the suite: 2015-02-28
  • Galaxy wrapper + owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rRNA
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA
  • Galaxy + wrapper version: 0.1
  • Conda id: hmmsearch3.0
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: rRNA + - description_md: '
  • Galaxy tool ids: racon
  • Description: + Consensus module for raw de novo DNA assembly of long uncorrected reads.
  • bio.tool + id: Racon
  • bio.tool ids: Racon
  • biii: + nan
  • bio.tool name: Racon
  • 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.
  • EDAM operation: Genome assembly, + Mapping assembly
  • EDAM topic: Whole genome sequencing, Sequence + assembly
  • Status: Up-to-date
  • Source: + https://github.com/isovic/racon
  • ToolShed categories: Sequence + Analysis
  • ToolShed id: racon
  • Date of first + commit of the suite: 2018-06-11
  • Galaxy wrapper owner: + bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/racon
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/racon
  • Galaxy + wrapper version: 1.5.0
  • Conda id: racon
  • Conda + version: 1.5.0
  • EDAM operation (no superclasses): + Genome assembly, Mapping assembly
  • EDAM topic (no superclasses): + Whole genome sequencing, Sequence assembly
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 27113
  • No. of tool users (all time) (usegalaxy.eu): 27315
  • Tool + usage (5 years) (usegalaxy.eu): 839
  • Tool usage (all time) + (usegalaxy.eu): 850
  • No. of tool users (5 years) (usegalaxy.org): + 9089
  • No. of tool users (all time) (usegalaxy.org): 9089
  • Tool + usage (5 years) (usegalaxy.org): 475
  • Tool usage (all time) + (usegalaxy.org): 475
  • No. of tool users (5 years) (usegalaxy.org.au): + 5452
  • No. of tool users (all time) (usegalaxy.org.au): 5452
  • Tool + usage (5 years) (usegalaxy.org.au): 171
  • Tool usage (all + time) (usegalaxy.org.au): 171
  • No. of tool users (5 years) + - all main servers: 41654
  • No. of tool users (all time) + - all main servers: 41856
  • Tool usage (5 years) - all main + servers: 1485
  • Tool usage (all time) - all main servers: + 1496
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: racon + - description_md: '
  • Galaxy tool ids: rasusa
  • Description: + Randomly subsample sequencing reads to a specified coverage
  • bio.tool + id: rasusa
  • bio.tool ids: rasusa
  • biii: + nan
  • bio.tool name: rasusa
  • bio.tool description: + Produces an unbiased subsample of your reads
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://github.com/mbhall88/rasusa
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: rasusa
  • Date + of first commit of the suite: 2024-02-16
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa
  • Galaxy + wrapper version: 2.0.0
  • Conda id: rasusa
  • Conda + version: 2.1.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 42
  • No. of tool + users (all time) (usegalaxy.eu): 42
  • Tool usage (5 years) + (usegalaxy.eu): 9
  • Tool usage (all time) (usegalaxy.eu): + 9
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 42
  • No. + of tool users (all time) - all main servers: 42
  • Tool usage + (5 years) - all main servers: 9
  • Tool usage (all time) - + all main servers: 9
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: rasusa + - description_md: '
  • Galaxy tool ids: raxml
  • Description: + RAxML - A Maximum Likelihood based phylogenetic inference
  • bio.tool + id: raxml
  • bio.tool ids: raxml
  • biii: + nan
  • bio.tool name: RAxML
  • bio.tool description: + A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
  • EDAM + operation: Sequence analysis, Phylogenetic tree analysis
  • EDAM + topic: Phylogenetics, Sequence analysis
  • Status: + To update
  • Source: http://www.exelixis-lab.org/web/software/raxml/
  • ToolShed + categories: Phylogenetics
  • ToolShed id: raxml
  • Date + of first commit of the suite: 2015-11-05
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml
  • Galaxy + wrapper version: 8.2.12
  • Conda id: raxml
  • Conda + version: 8.2.13
  • EDAM operation (no superclasses): + Sequence analysis
  • EDAM topic (no superclasses): Phylogenetics
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 10905
  • No. of tool + users (all time) (usegalaxy.eu): 10905
  • Tool usage (5 years) + (usegalaxy.eu): 966
  • Tool usage (all time) (usegalaxy.eu): + 966
  • No. of tool users (5 years) (usegalaxy.org): 5100
  • No. + of tool users (all time) (usegalaxy.org): 5114
  • Tool usage + (5 years) (usegalaxy.org): 587
  • Tool usage (all time) (usegalaxy.org): + 587
  • No. of tool users (5 years) (usegalaxy.org.au): 4955
  • No. + of tool users (all time) (usegalaxy.org.au): 6094
  • Tool + usage (5 years) (usegalaxy.org.au): 765
  • Tool usage (all + time) (usegalaxy.org.au): 892
  • No. of tool users (5 years) + - all main servers: 20960
  • No. of tool users (all time) + - all main servers: 22113
  • Tool usage (5 years) - all main + servers: 2318
  • Tool usage (all time) - all main servers: + 2445
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: raxml + - description_md: '
  • Galaxy tool ids: read_it_and_keep
  • Description: + Rapid decontamination of SARS-CoV-2 sequencing reads
  • bio.tool + id: read_it_and_keep
  • bio.tool ids: read_it_and_keep
  • biii: + nan
  • bio.tool name: read_it_and_keep
  • bio.tool + description: Read contamination removal
  • EDAM operation: + Filtering, Genome alignment
  • EDAM topic: Pathology, Genomics
  • Status: + To update
  • Source: https://github.com/GenomePathogenAnalysisService/read-it-and-keep
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: read_it_and_keep
  • Date + of first commit of the suite: 2022-01-28
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep
  • Galaxy + wrapper version: 0.2.2
  • Conda id: read-it-and-keep
  • Conda + version: 0.3.0
  • EDAM operation (no superclasses): + Filtering, Genome alignment
  • EDAM topic (no superclasses): + Pathology, Genomics
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 3710
  • No. of tool users (all time) (usegalaxy.eu): 3710
  • Tool + usage (5 years) (usegalaxy.eu): 80
  • Tool usage (all time) + (usegalaxy.eu): 80
  • No. of tool users (5 years) (usegalaxy.org): + 7
  • No. of tool users (all time) (usegalaxy.org): 7
  • Tool + usage (5 years) (usegalaxy.org): 6
  • Tool usage (all time) + (usegalaxy.org): 6
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 3717
  • No. of tool users (all time) - all main + servers: 3717
  • Tool usage (5 years) - all main servers: + 86
  • Tool usage (all time) - all main servers: 86
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: read_it_and_keep + - description_md: '
  • Galaxy tool ids: reago
  • Description: + Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.
  • bio.tool + id: reago
  • bio.tool ids: reago
  • biii: + nan
  • bio.tool name: REAGO
  • bio.tool description: + This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.
  • EDAM + operation: Sequence assembly
  • EDAM topic: Sequence + assembly, RNA, Metagenomics, Microbiology
  • Status: Up-to-date
  • Source: + https://github.com/chengyuan/reago-1.1
  • ToolShed categories: + Metagenomics, RNA
  • ToolShed id: reago
  • Date + of first commit of the suite: 2015-12-09
  • Galaxy wrapper + owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago
  • Galaxy + wrapper version: 1.1
  • Conda id: reago
  • Conda + version: 1.1
  • EDAM operation (no superclasses): Sequence + assembly
  • EDAM topic (no superclasses): Sequence assembly, + RNA, Metagenomics, Microbiology
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: reago + - description_md: '
  • Galaxy tool ids: recentrifuge
  • 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."
  • bio.tool + id: Recentrifuge
  • bio.tool ids: Recentrifuge
  • biii: + nan
  • bio.tool name: Recentrifuge
  • bio.tool + description: Robust comparative analysis and contamination removal for + metagenomics.
  • EDAM operation: Taxonomic classification, + Expression analysis, Cross-assembly
  • EDAM topic: Metagenomics, + Microbial ecology, Metagenomic sequencing
  • Status: Up-to-date
  • Source: + https://github.com/khyox/recentrifuge
  • ToolShed categories: + Metagenomics
  • ToolShed id: recentrifuge
  • Date + of first commit of the suite: 2022-05-04
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge
  • Galaxy + wrapper version: 1.15.0
  • Conda id: recentrifuge
  • Conda + version: 1.15.0
  • EDAM operation (no superclasses): + Taxonomic classification, Expression analysis, Cross-assembly
  • EDAM + topic (no superclasses): Metagenomics, Microbial ecology, Metagenomic + sequencing
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 472
  • No. of tool + users (all time) (usegalaxy.eu): 472
  • Tool usage (5 years) + (usegalaxy.eu): 92
  • Tool usage (all time) (usegalaxy.eu): + 92
  • No. of tool users (5 years) (usegalaxy.org): 32
  • No. + of tool users (all time) (usegalaxy.org): 32
  • Tool usage + (5 years) (usegalaxy.org): 13
  • Tool usage (all time) (usegalaxy.org): + 13
  • No. of tool users (5 years) (usegalaxy.org.au): 6
  • No. + of tool users (all time) (usegalaxy.org.au): 6
  • Tool usage + (5 years) (usegalaxy.org.au): 4
  • Tool usage (all time) (usegalaxy.org.au): + 4
  • No. of tool users (5 years) - all main servers: 510
  • No. + of tool users (all time) - all main servers: 510
  • Tool usage + (5 years) - all main servers: 109
  • Tool usage (all time) + - all main servers: 109
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: recentrifuge + - description_md: '
  • Galaxy tool ids: repeatexplorer_clustering
  • Description: + Tool for annotation of repeats from unassembled shotgun reads.
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/repeatexplorer/repex_tarean
  • ToolShed + categories: Genome annotation
  • ToolShed id: repeatexplorer2
  • Date + of first commit of the suite: 2023-11-01
  • Galaxy wrapper + owner: gga
  • Galaxy wrapper source: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2
  • Galaxy + wrapper parsed folder: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2
  • Galaxy + wrapper version: 2.3.8
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 95
  • No. of tool users (all time) (usegalaxy.eu): 95
  • Tool + usage (5 years) (usegalaxy.eu): 38
  • Tool usage (all time) + (usegalaxy.eu): 38
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 95
  • No. of tool users (all time) - all main + servers: 95
  • Tool usage (5 years) - all main servers: + 38
  • Tool usage (all time) - all main servers: 38
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: repeatexplorer2 + - description_md: '
  • Galaxy tool ids: roary
  • Description: + Roary the pangenome pipeline
  • bio.tool id: roary
  • bio.tool + ids: roary
  • biii: nan
  • bio.tool name: + Roary
  • 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.
  • EDAM operation: + Genome assembly
  • EDAM topic: DNA, Genomics, Mapping
  • Status: + Up-to-date
  • Source: https://sanger-pathogens.github.io/Roary/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: roary
  • Date + of first commit of the suite: 2017-06-21
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary
  • Galaxy + wrapper version: 3.13.0
  • Conda id: roary
  • Conda + version: 3.13.0
  • EDAM operation (no superclasses): + Genome assembly
  • EDAM topic (no superclasses): DNA, Genomics, + Mapping
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 15196
  • No. of tool + users (all time) (usegalaxy.eu): 15685
  • Tool usage (5 years) + (usegalaxy.eu): 1459
  • Tool usage (all time) (usegalaxy.eu): + 1501
  • No. of tool users (5 years) (usegalaxy.org): 12188
  • No. + of tool users (all time) (usegalaxy.org): 12188
  • Tool usage + (5 years) (usegalaxy.org): 1768
  • Tool usage (all time) (usegalaxy.org): + 1768
  • No. of tool users (5 years) (usegalaxy.org.au): 4881
  • No. + of tool users (all time) (usegalaxy.org.au): 5539
  • Tool + usage (5 years) (usegalaxy.org.au): 518
  • Tool usage (all + time) (usegalaxy.org.au): 555
  • No. of tool users (5 years) + - all main servers: 32265
  • No. of tool users (all time) + - all main servers: 33412
  • Tool usage (5 years) - all main + servers: 3745
  • Tool usage (all time) - all main servers: + 3824
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: roary + - description_md: '
  • 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
  • Description: + an RNA-seq quality control package
  • bio.tool id: rseqc
  • bio.tool + ids: rseqc
  • biii: nan
  • bio.tool name: + RSeQC
  • 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.
  • EDAM operation: + Data handling
  • EDAM topic: Sequencing
  • Status: + To update
  • Source: https://code.google.com/p/rseqc/
  • ToolShed + categories: Convert Formats, Sequence Analysis, RNA, Transcriptomics, + Visualization
  • ToolShed id: rseqc
  • Date of + first commit of the suite: 2017-02-27
  • Galaxy wrapper owner: + nilesh
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc
  • Galaxy + wrapper version: 5.0.3
  • Conda id: rseqc
  • Conda + version: 5.0.4
  • EDAM operation (no superclasses): + Data handling
  • EDAM topic (no superclasses): Sequencing
  • Available + on UseGalaxy.org (Main): 22
  • Available on UseGalaxy.org.au: + 22
  • Available on UseGalaxy.eu: 22
  • Available + on UseGalaxy.fr: 22
  • Tools available on UseGalaxy.org (Main): + 22
  • Tools available on UseGalaxy.org.au: 22
  • Tools + available on UseGalaxy.eu: 22
  • Tools available on UseGalaxy.fr: + 22
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 22
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 136315
  • No. of tool + users (all time) (usegalaxy.eu): 147595
  • Tool usage (5 years) + (usegalaxy.eu): 8341
  • Tool usage (all time) (usegalaxy.eu): + 9385
  • No. of tool users (5 years) (usegalaxy.org): 138707
  • No. + of tool users (all time) (usegalaxy.org): 161046
  • Tool usage + (5 years) (usegalaxy.org): 10696
  • Tool usage (all time) + (usegalaxy.org): 12789
  • No. of tool users (5 years) (usegalaxy.org.au): + 22718
  • No. of tool users (all time) (usegalaxy.org.au): + 23767
  • Tool usage (5 years) (usegalaxy.org.au): 1593
  • Tool + usage (all time) (usegalaxy.org.au): 1695
  • No. of tool users + (5 years) - all main servers: 297740
  • No. of tool users + (all time) - all main servers: 332408
  • Tool usage (5 years) + - all main servers: 20630
  • Tool usage (all time) - all main + servers: 23869
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: rseqc + - description_md: '
  • Galaxy tool ids: alevin, salmon, salmonquantmerge
  • Description: + Salmon is a wicked-fast program to produce a highly-accurate, transcript-level + quantification estimates from RNA-seq and single-cell data.
  • bio.tool + id: salmon
  • bio.tool ids: salmon
  • biii: + nan
  • bio.tool name: Salmon
  • bio.tool description: + A tool for transcript expression quantification from RNA-seq data
  • EDAM + operation: Sequence composition calculation, RNA-Seq quantification, + Gene expression analysis
  • EDAM topic: RNA-Seq, Gene expression, + Transcriptomics
  • Status: To update
  • Source: + https://github.com/COMBINE-lab/salmon
  • ToolShed categories: + Sequence Analysis, RNA, Transcriptomics
  • ToolShed id: nan
  • Date + of first commit of the suite: 2019-09-18
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/salmon
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/salmon
  • Galaxy + wrapper version: 1.10.1
  • Conda id: salmon
  • Conda + version: 1.10.3
  • EDAM operation (no superclasses): + Sequence composition calculation, RNA-Seq quantification, Gene expression analysis
  • EDAM + topic (no superclasses): RNA-Seq, Transcriptomics
  • Available + on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: + 2
  • Available on UseGalaxy.eu: 3
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools + available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available 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.no: + 3
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 73085
  • No. of tool + users (all time) (usegalaxy.eu): 77081
  • Tool usage (5 years) + (usegalaxy.eu): 2243
  • Tool usage (all time) (usegalaxy.eu): + 2319
  • No. of tool users (5 years) (usegalaxy.org): 90634
  • No. + of tool users (all time) (usegalaxy.org): 122835
  • Tool usage + (5 years) (usegalaxy.org): 3402
  • Tool usage (all time) (usegalaxy.org): + 4726
  • No. of tool users (5 years) (usegalaxy.org.au): 13371
  • No. + of tool users (all time) (usegalaxy.org.au): 15818
  • Tool + usage (5 years) (usegalaxy.org.au): 513
  • Tool usage (all + time) (usegalaxy.org.au): 586
  • No. of tool users (5 years) + - all main servers: 177090
  • No. of tool users (all time) + - all main servers: 215734
  • Tool usage (5 years) - all main + servers: 6158
  • Tool usage (all time) - all main servers: + 7631
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: salmon + - description_md: '
  • Galaxy tool ids: sarscov2formatter
  • Description: + sarscov2formatter custom script
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: + https://github.com/nickeener/sarscov2formatter
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: sarscov2formatter
  • Date + of first commit of the suite: 2020-05-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter
  • Galaxy + wrapper version: 1.0
  • Conda id: sarscov2formatter
  • Conda + version: 1.0
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 174
  • No. of tool users (all time) (usegalaxy.eu): 174
  • Tool + usage (5 years) (usegalaxy.eu): 16
  • Tool usage (all time) + (usegalaxy.eu): 16
  • No. of tool users (5 years) (usegalaxy.org): + 399
  • No. of tool users (all time) (usegalaxy.org): 399
  • Tool + usage (5 years) (usegalaxy.org): 29
  • Tool usage (all time) + (usegalaxy.org): 29
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 573
  • No. of tool users (all time) - all main + servers: 573
  • Tool usage (5 years) - all main servers: + 45
  • Tool usage (all time) - all main servers: 45
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: sarscov2formatter + - description_md: '
  • Galaxy tool ids: sarscov2summary
  • Description: + sarscov2summary custom script
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://github.com/nickeener/sarscov2summary
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: sarscov2summary
  • Date + of first commit of the suite: 2020-05-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary
  • Galaxy + wrapper version: 0.1
  • Conda id: sarscov2summary
  • Conda + version: 0.5
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 140
  • No. of tool users (all time) (usegalaxy.eu): 140
  • Tool + usage (5 years) (usegalaxy.eu): 5
  • Tool usage (all time) + (usegalaxy.eu): 5
  • No. of tool users (5 years) (usegalaxy.org): + 253
  • No. of tool users (all time) (usegalaxy.org): 253
  • Tool + usage (5 years) (usegalaxy.org): 6
  • Tool usage (all time) + (usegalaxy.org): 6
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 393
  • No. of tool users (all time) - all main + servers: 393
  • Tool usage (5 years) - all main servers: + 11
  • Tool usage (all time) - all main servers: 11
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: sarscov2summary + - description_md: '
  • Galaxy tool ids: scoary
  • Description: + Scoary calculates the assocations between all genes in the accessory genome + and the traits.
  • bio.tool id: scoary
  • bio.tool + ids: scoary
  • biii: nan
  • bio.tool name: + Scoary
  • 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.
  • EDAM operation: Analysis
  • EDAM + topic: Genotype and phenotype, Model organisms, GWAS study, Functional + genomics
  • Status: Up-to-date
  • Source: + https://github.com/AdmiralenOla/Scoary
  • ToolShed categories: + Metagenomics
  • ToolShed id: scoary
  • Date of + first commit of the suite: 2021-03-18
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary
  • Galaxy + wrapper version: 1.6.16
  • Conda id: scoary
  • Conda + version: 1.6.16
  • EDAM operation (no superclasses): + Analysis
  • EDAM topic (no superclasses): Genotype and phenotype, + Model organisms, GWAS study, Functional genomics
  • Available on + UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 901
  • No. of tool + users (all time) (usegalaxy.eu): 901
  • Tool usage (5 years) + (usegalaxy.eu): 90
  • Tool usage (all time) (usegalaxy.eu): + 90
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 901
  • No. + of tool users (all time) - all main servers: 901
  • Tool usage + (5 years) - all main servers: 90
  • Tool usage (all time) + - all main servers: 90
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: scoary + - description_md: '
  • Galaxy tool ids: semibin_bin, semibin_concatenate_fasta, + semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, + semibin_train
  • Description: SemiBin: Semi-supervised Metagenomic + Binning Using Siamese Neural Networks
  • bio.tool id: semibin
  • bio.tool + ids: semibin
  • biii: nan
  • bio.tool name: + SemiBin
  • bio.tool description: Command tool for metagenomic + binning with semi-supervised deep learning using information from reference + genomes.
  • EDAM operation: Sequence assembly, Read binning
  • EDAM + topic: Metagenomics, Machine learning, Microbial ecology, Sequence assembly
  • Status: + To update
  • Source: https://semibin.readthedocs.io/en/latest/
  • ToolShed + categories: Metagenomics
  • ToolShed id: semibin
  • Date + of first commit of the suite: 2022-10-14
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin
  • Galaxy + wrapper version: 2.0.2
  • Conda id: semibin
  • Conda + version: 2.1.0
  • EDAM operation (no superclasses): + Sequence assembly, Read binning
  • EDAM topic (no superclasses): + Metagenomics, Machine learning, Microbial ecology, Sequence assembly
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 6
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 6
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 931
  • No. of tool + users (all time) (usegalaxy.eu): 931
  • Tool usage (5 years) + (usegalaxy.eu): 93
  • Tool usage (all time) (usegalaxy.eu): + 93
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 931
  • No. + of tool users (all time) - all main servers: 931
  • Tool usage + (5 years) - all main servers: 93
  • Tool usage (all time) + - all main servers: 93
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: semibin + - description_md: '
  • Galaxy tool ids: seqkit_fx2tab, seqkit_locate, + seqkit_sort, seqkit_stats, seqkit_translate
  • Description: + A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  • bio.tool + id: seqkit
  • bio.tool ids: seqkit
  • biii: + nan
  • bio.tool name: seqkit
  • 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.
  • EDAM operation: DNA + transcription, Sequence trimming, DNA translation, Sequence conversion
  • EDAM + topic: Database management, Sequence analysis
  • Status: + Up-to-date
  • Source: https://bioinf.shenwei.me/seqkit/
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: seqkit
  • Date + of first commit of the suite: 2022-06-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit
  • Galaxy + wrapper version: 2.8.2
  • Conda id: seqkit
  • Conda + version: 2.8.2
  • EDAM operation (no superclasses): + DNA transcription, Sequence trimming, DNA translation
  • EDAM topic + (no superclasses): Database management, Sequence analysis
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 2
  • Available on UseGalaxy.eu: 5
  • Available + on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 2
  • Tools + available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: + 3
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 3364
  • No. of tool + users (all time) (usegalaxy.eu): 3364
  • Tool usage (5 years) + (usegalaxy.eu): 247
  • Tool usage (all time) (usegalaxy.eu): + 247
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 244
  • No. + of tool users (all time) (usegalaxy.org.au): 244
  • Tool usage + (5 years) (usegalaxy.org.au): 33
  • Tool usage (all time) + (usegalaxy.org.au): 33
  • No. of tool users (5 years) - all + main servers: 3608
  • No. of tool users (all time) - all main + servers: 3608
  • Tool usage (5 years) - all main servers: + 280
  • Tool usage (all time) - all main servers: 280
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: seqkit + - description_md: '
  • Galaxy tool ids: seqprep
  • Description: + Tool for merging paired-end Illumina reads and trimming adapters.
  • bio.tool + id: seqprep
  • bio.tool ids: seqprep
  • biii: + nan
  • bio.tool name: SeqPrep
  • bio.tool description: + Strips adapters and optionally merges overlapping paired-end (or paired-end + contamination in mate-pair libraries) illumina style reads.
  • EDAM + operation: Nucleic acid design
  • EDAM topic: Genomics, + Sequence assembly, Sequencing, Probes and primers
  • Status: + Up-to-date
  • Source: https://github.com/jstjohn/SeqPrep
  • ToolShed + categories: Fastq Manipulation, Sequence Analysis
  • ToolShed + id: seqprep
  • Date of first commit of the suite: 2024-01-15
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep
  • Galaxy + wrapper version: 1.3.2
  • Conda id: seqprep
  • Conda + version: 1.3.2
  • EDAM operation (no superclasses): + Nucleic acid design
  • EDAM topic (no superclasses): Genomics, + Sequence assembly, Sequencing, Probes and primers
  • Available on + UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 2424
  • No. of tool + users (all time) (usegalaxy.eu): 2424
  • Tool usage (5 years) + (usegalaxy.eu): 102
  • Tool usage (all time) (usegalaxy.eu): + 102
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 2424
  • No. + of tool users (all time) - all main servers: 2424
  • Tool + usage (5 years) - all main servers: 102
  • Tool usage (all + time) - all main servers: 102
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: seqprep + - description_md: '
  • Galaxy tool ids: seqsero2
  • Description: + Salmonella serotype prediction from genome sequencing data
  • bio.tool + id: seqsero2
  • bio.tool ids: seqsero2
  • biii: + nan
  • bio.tool name: SeqSero2
  • 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)
  • EDAM operation: Genome indexing, Antimicrobial + resistance prediction, Genome alignment
  • EDAM topic: Whole + genome sequencing, Sequence assembly, Genomics
  • Status: + Up-to-date
  • Source: https://github.com/denglab/SeqSero2
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: seqsero2
  • Date + of first commit of the suite: 2023-11-07
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2
  • Galaxy + wrapper version: 1.3.1
  • Conda id: seqsero2
  • Conda + version: 1.3.1
  • EDAM operation (no superclasses): + Genome indexing, Antimicrobial resistance prediction, Genome alignment
  • EDAM + topic (no superclasses): Whole genome sequencing, Sequence assembly, + Genomics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 4182
  • No. of tool + users (all time) (usegalaxy.eu): 4182
  • Tool usage (5 years) + (usegalaxy.eu): 42
  • Tool usage (all time) (usegalaxy.eu): + 42
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 4182
  • No. + of tool users (all time) - all main servers: 4182
  • Tool + usage (5 years) - all main servers: 42
  • Tool usage (all + time) - all main servers: 42
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: seqsero2 + - description_md: '
  • Galaxy tool ids: shorah_amplicon
  • Description: + Reconstruct haplotypes using ShoRAH in amplicon mode
  • bio.tool + id: shorah
  • bio.tool ids: shorah
  • biii: + nan
  • bio.tool name: ShoRAH
  • 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.
  • EDAM operation: + Haplotype mapping, Variant calling
  • EDAM topic: Metagenomics, + Sequencing, Genetics
  • Status: To update
  • Source: + https://github.com/cbg-ethz/shorah/blob/master/README.md
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: shorah_amplicon
  • Date + of first commit of the suite: 2018-11-27
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah
  • Galaxy + wrapper version: 1.1.3
  • Conda id: shorah
  • Conda + version: 1.99.2
  • EDAM operation (no superclasses): + Haplotype mapping, Variant calling
  • EDAM topic (no superclasses): + Metagenomics, Sequencing, Genetics
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: shorah + - description_md: '
  • Galaxy tool ids: shovill
  • Description: + Faster de novo assembly pipeline based around Spades
  • bio.tool + id: shovill
  • bio.tool ids: shovill
  • biii: + nan
  • bio.tool name: shovill
  • 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.
  • EDAM + operation: Genome assembly
  • EDAM topic: Genomics, + Microbiology, Sequence assembly
  • Status: Up-to-date
  • Source: + https://github.com/tseemann/shovill
  • ToolShed categories: + Assembly
  • ToolShed id: shovill
  • Date of first + commit of the suite: 2017-10-24
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill
  • Galaxy + wrapper version: 1.1.0
  • Conda id: shovill
  • Conda + version: 1.1.0
  • EDAM operation (no superclasses): + Genome assembly
  • EDAM topic (no superclasses): Genomics, + Microbiology, Sequence assembly
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 46125
  • No. of tool users (all time) (usegalaxy.eu): 47376
  • Tool + usage (5 years) (usegalaxy.eu): 2273
  • Tool usage (all time) + (usegalaxy.eu): 2356
  • No. of tool users (5 years) (usegalaxy.org): + 40577
  • No. of tool users (all time) (usegalaxy.org): 40577
  • Tool + usage (5 years) (usegalaxy.org): 3971
  • Tool usage (all time) + (usegalaxy.org): 3971
  • No. of tool users (5 years) (usegalaxy.org.au): + 19960
  • No. of tool users (all time) (usegalaxy.org.au): + 21130
  • Tool usage (5 years) (usegalaxy.org.au): 1085
  • Tool + usage (all time) (usegalaxy.org.au): 1199
  • No. of tool users + (5 years) - all main servers: 106662
  • No. of tool users + (all time) - all main servers: 109083
  • Tool usage (5 years) + - all main servers: 7329
  • Tool usage (all time) - all main + servers: 7526
  • Reviewed: True
  • To keep: + True
  • Deprecated: False
' + title_md: shovill + - description_md: '
  • Galaxy tool ids: sistr_cmd
  • Description: + SISTR in silico serotyping tool
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://github.com/phac-nml/sistr_cmd
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: sistr_cmd
  • Date + of first commit of the suite: 2017-02-20
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: nan
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd
  • Galaxy + wrapper version: 1.1.1
  • Conda id: sistr_cmd
  • Conda + version: 1.1.2
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 3457
  • No. of tool + users (all time) (usegalaxy.eu): 3457
  • Tool usage (5 years) + (usegalaxy.eu): 301
  • Tool usage (all time) (usegalaxy.eu): + 301
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 556
  • No. + of tool users (all time) (usegalaxy.org.au): 556
  • Tool usage + (5 years) (usegalaxy.org.au): 65
  • Tool usage (all time) + (usegalaxy.org.au): 65
  • No. of tool users (5 years) - all + main servers: 4013
  • No. of tool users (all time) - all main + servers: 4013
  • Tool usage (5 years) - all main servers: + 366
  • Tool usage (all time) - all main servers: 366
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: sistr_cmd + - description_md: '
  • Galaxy tool ids: smgu_frameshift_deletions_checks
  • Description: + Set of utilities for manipulating small viral genome data.
  • bio.tool + id: v-pipe
  • bio.tool ids: v-pipe
  • biii: + nan
  • bio.tool name: V-pipe
  • bio.tool description: + Bioinformatics pipeline for the analysis of next-generation sequencing data + derived from intra-host viral populations.
  • EDAM operation: + Read pre-processing, Sequence alignment, Genetic variation analysis
  • EDAM + topic: Genomics, Population genetics, Workflows, Virology, Sequencing
  • Status: + Up-to-date
  • Source: https://github.com/cbg-ethz/smallgenomeutilities
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: smallgenomeutilities
  • Date + of first commit of the suite: 2023-05-30
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities
  • Galaxy + wrapper version: 0.4.1
  • Conda id: smallgenomeutilities
  • Conda + version: 0.4.1
  • EDAM operation (no superclasses): + Read pre-processing, Sequence alignment, Genetic variation analysis
  • EDAM + topic (no superclasses): Genomics, Population genetics, Workflows, Virology, + Sequencing
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 158
  • No. of tool + users (all time) (usegalaxy.eu): 158
  • Tool usage (5 years) + (usegalaxy.eu): 8
  • Tool usage (all time) (usegalaxy.eu): + 8
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 158
  • No. + of tool users (all time) - all main servers: 158
  • Tool usage + (5 years) - all main servers: 8
  • Tool usage (all time) - + all main servers: 8
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: smallgenomeutilities + - description_md: '
  • Galaxy tool ids: smalt
  • Description: + SMALT aligns DNA sequencing reads with a reference genome.
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: Up-to-date
  • Source: http://www.sanger.ac.uk/science/tools/smalt-0
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: smalt
  • Date + of first commit of the suite: 2017-09-19
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://sourceforge.net/projects/smalt/
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt
  • Galaxy + wrapper version: 0.7.6
  • Conda id: smalt
  • Conda + version: 0.7.6
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: smalt + - description_md: '
  • Galaxy tool ids: snap, snap_training
  • Description: + SNAP is a general purpose gene finding program suitable for both eukaryotic + and prokaryotic genomes.
  • bio.tool id: snap
  • bio.tool + ids: snap
  • biii: nan
  • bio.tool name: + SNAP
  • bio.tool description: The Semi-HMM-based Nucleic Acid + Parser is a gene prediction tool.
  • EDAM operation: Gene + prediction
  • EDAM topic: DNA, DNA polymorphism, Genetics
  • Status: + Up-to-date
  • Source: https://github.com/KorfLab/SNAP
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: snap
  • Date + of first commit of the suite: 2017-10-12
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap
  • Galaxy + wrapper version: 2013_11_29
  • Conda id: snap
  • Conda + version: 2013_11_29
  • EDAM operation (no superclasses): + Gene prediction
  • EDAM topic (no superclasses): DNA polymorphism, + Genetics
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1499
  • No. of tool + users (all time) (usegalaxy.eu): 1638
  • Tool usage (5 years) + (usegalaxy.eu): 331
  • Tool usage (all time) (usegalaxy.eu): + 358
  • No. of tool users (5 years) (usegalaxy.org): 779
  • No. + of tool users (all time) (usegalaxy.org): 779
  • Tool usage + (5 years) (usegalaxy.org): 244
  • Tool usage (all time) (usegalaxy.org): + 244
  • No. of tool users (5 years) (usegalaxy.org.au): 467
  • No. + of tool users (all time) (usegalaxy.org.au): 467
  • Tool usage + (5 years) (usegalaxy.org.au): 83
  • Tool usage (all time) + (usegalaxy.org.au): 83
  • No. of tool users (5 years) - all + main servers: 2745
  • No. of tool users (all time) - all main + servers: 2884
  • Tool usage (5 years) - all main servers: + 658
  • Tool usage (all time) - all main servers: 685
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: snap + - description_md: '
  • Galaxy tool ids: snippy_core, snippy, snippy_clean_full_aln
  • Description: + Contains the snippy tool for characterising microbial snps
  • bio.tool + id: snippy
  • bio.tool ids: snippy
  • biii: + nan
  • bio.tool name: snippy
  • bio.tool description: + Rapid haploid variant calling and core SNP phylogeny generation.
  • EDAM + operation: Phylogenetic tree visualisation, Phylogenetic tree generation, + Variant calling
  • EDAM topic: Genomics, Model organisms, + DNA polymorphism, Phylogenetics
  • Status: To update
  • Source: + https://github.com/tseemann/snippy
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: snippy
  • Date + of first commit of the suite: 2019-04-02
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy
  • Galaxy + wrapper version: nan
  • Conda id: snippy
  • Conda + version: 4.6.0
  • EDAM operation (no superclasses): + Phylogenetic tree visualisation, Variant calling
  • EDAM topic (no + superclasses): Genomics, Model organisms, DNA polymorphism, Phylogenetics
  • Available + on UseGalaxy.org (Main): 3
  • Available on UseGalaxy.org.au: + 3
  • Available on UseGalaxy.eu: 3
  • Available + on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): + 3
  • Tools available on UseGalaxy.org.au: 3
  • Tools + available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: + 3
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 121363
  • No. of tool + users (all time) (usegalaxy.eu): 124773
  • Tool usage (5 years) + (usegalaxy.eu): 3448
  • Tool usage (all time) (usegalaxy.eu): + 3602
  • No. of tool users (5 years) (usegalaxy.org): 92504
  • No. + of tool users (all time) (usegalaxy.org): 92504
  • Tool usage + (5 years) (usegalaxy.org): 3945
  • Tool usage (all time) (usegalaxy.org): + 3945
  • No. of tool users (5 years) (usegalaxy.org.au): 48068
  • No. + of tool users (all time) (usegalaxy.org.au): 52034
  • Tool + usage (5 years) (usegalaxy.org.au): 2705
  • Tool usage (all + time) (usegalaxy.org.au): 3073
  • No. of tool users (5 years) + - all main servers: 261935
  • No. of tool users (all time) + - all main servers: 269311
  • Tool usage (5 years) - all main + servers: 10098
  • Tool usage (all time) - all main servers: + 10620
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: snippy + - description_md: '
  • Galaxy tool ids: sonneityping
  • Description: + Scripts for parsing Mykrobe predict results for Shigella sonnei.
  • bio.tool + id: sonneityping
  • bio.tool ids: sonneityping
  • biii: + nan
  • bio.tool name: sonneityping
  • bio.tool + description: Scripts for parsing Mykrobe predict results for Shigella + sonnei.
  • EDAM operation: Antimicrobial resistance prediction, + Variant calling, Genotyping
  • EDAM topic: Whole genome sequencing, + Genotype and phenotype, Genetic variation, Metagenomics
  • Status: + Up-to-date
  • Source: https://github.com/katholt/sonneityping
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: sonneityping
  • Date + of first commit of the suite: 2021-09-16
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/katholt/sonneityping
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping
  • Galaxy + wrapper version: 20210201
  • Conda id: sonneityping
  • Conda + version: 20210201
  • EDAM operation (no superclasses): + Antimicrobial resistance prediction, Variant calling, Genotyping
  • EDAM + topic (no superclasses): Whole genome sequencing, Genotype and phenotype, + Genetic variation, Metagenomics
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1
  • No. of tool users (all time) (usegalaxy.eu): 1
  • Tool + usage (5 years) (usegalaxy.eu): 1
  • Tool usage (all time) + (usegalaxy.eu): 1
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 1
  • No. of tool users (all time) - all main + servers: 1
  • Tool usage (5 years) - all main servers: + 1
  • Tool usage (all time) - all main servers: 1
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: sonneityping + - description_md: '
  • Galaxy tool ids: bg_sortmerna
  • Description: + SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from + metatransriptomic data produced by next-generation sequencers.
  • bio.tool + id: sortmerna
  • bio.tool ids: sortmerna
  • biii: + nan
  • bio.tool name: SortMeRNA
  • bio.tool description: + Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
  • EDAM + operation: Sequence similarity search, Sequence comparison, Sequence + alignment analysis
  • EDAM topic: Metatranscriptomics, Metagenomics
  • Status: + To update
  • Source: http://bioinfo.lifl.fr/RNA/sortmerna/
  • ToolShed + categories: RNA
  • ToolShed id: sortmerna
  • Date + of first commit of the suite: 2016-03-17
  • Galaxy wrapper + owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna
  • Galaxy + wrapper version: 4.3.6
  • Conda id: sortmerna
  • Conda + version: 4.3.7
  • EDAM operation (no superclasses): + Sequence similarity search, Sequence alignment analysis
  • EDAM topic + (no superclasses): Metatranscriptomics, Metagenomics
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 19865
  • No. of tool + users (all time) (usegalaxy.eu): 21034
  • Tool usage (5 years) + (usegalaxy.eu): 1047
  • Tool usage (all time) (usegalaxy.eu): + 1126
  • No. of tool users (5 years) (usegalaxy.org): 3141
  • No. + of tool users (all time) (usegalaxy.org): 3141
  • Tool usage + (5 years) (usegalaxy.org): 328
  • Tool usage (all time) (usegalaxy.org): + 328
  • No. of tool users (5 years) (usegalaxy.org.au): 3304
  • No. + of tool users (all time) (usegalaxy.org.au): 3304
  • Tool + usage (5 years) (usegalaxy.org.au): 189
  • Tool usage (all + time) (usegalaxy.org.au): 189
  • No. of tool users (5 years) + - all main servers: 26310
  • No. of tool users (all time) + - all main servers: 27479
  • Tool usage (5 years) - all main + servers: 1564
  • Tool usage (all time) - all main servers: + 1643
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: sortmerna + - description_md: "
  • Galaxy tool ids: spades_biosyntheticspades,\ + \ spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades,\ + \ spades_plasmidspades, rnaspades, spades_rnaviralspades, spades
  • 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.
  • bio.tool id:\ + \ spades
  • bio.tool ids: plasmidspades, metaplasmidspades,\ + \ rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades,\ + \ rnaviralspades
  • biii: nan
  • bio.tool name:\ + \ SPAdes
  • 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.
  • EDAM\ + \ operation: Genome assembly
  • EDAM topic: Sequence\ + \ assembly
  • Status: To update
  • Source:\ + \ https://github.com/ablab/spades
  • ToolShed categories:\ + \ Assembly, RNA, Metagenomics
  • ToolShed id: spades
  • Date\ + \ of first commit of the suite: 2017-06-30
  • Galaxy wrapper\ + \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades
  • Galaxy\ + \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades
  • Galaxy\ + \ wrapper version: 3.15.5
  • Conda id: spades
  • Conda\ + \ version: 4.0.0
  • EDAM operation (no superclasses):\ + \ Genome assembly
  • EDAM topic (no superclasses): Sequence\ + \ assembly
  • Available on UseGalaxy.org (Main): 9
  • Available\ + \ on UseGalaxy.org.au: 9
  • Available on UseGalaxy.eu:\ + \ 9
  • Available on UseGalaxy.fr: 9
  • Tools available\ + \ on UseGalaxy.org (Main): 9
  • Tools available on UseGalaxy.org.au:\ + \ 9
  • Tools available on UseGalaxy.eu: 9
  • Tools\ + \ available on UseGalaxy.fr: 9
  • Tools available on APOSTL:\ + \ 0
  • Tools available on ARGs-OAP: 0
  • Tools\ + \ available on CIRM-CFBP: 0
  • Tools available on ChemFlow:\ + \ 0
  • Tools available 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.no: 3
  • Tools\ + \ available on Viral Variant Visualizer (VVV): 0
  • No. of\ + \ tool users (5 years) (usegalaxy.eu): 82716
  • No. of tool\ + \ users (all time) (usegalaxy.eu): 87113
  • Tool usage (5\ + \ years) (usegalaxy.eu): 8209
  • Tool usage (all time) (usegalaxy.eu):\ + \ 8526
  • No. of tool users (5 years) (usegalaxy.org): 120471
  • No.\ + \ of tool users (all time) (usegalaxy.org): 120475
  • Tool\ + \ usage (5 years) (usegalaxy.org): 14787
  • Tool usage (all\ + \ time) (usegalaxy.org): 14790
  • No. of tool users (5 years)\ + \ (usegalaxy.org.au): 54067
  • No. of tool users (all time)\ + \ (usegalaxy.org.au): 61541
  • Tool usage (5 years) (usegalaxy.org.au):\ + \ 5817
  • Tool usage (all time) (usegalaxy.org.au): 6653
  • No.\ + \ of tool users (5 years) - all main servers: 257254
  • No.\ + \ of tool users (all time) - all main servers: 269129
  • Tool\ + \ usage (5 years) - all main servers: 28813
  • Tool usage\ + \ (all time) - all main servers: 29969
  • Reviewed:\ + \ True
  • To keep: True
  • Deprecated: False
" + title_md: spades + - description_md: '
  • Galaxy tool ids: spotyping
  • Description: + SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from + sequence reads
  • bio.tool id: spotyping
  • bio.tool + ids: spotyping
  • biii: nan
  • bio.tool + name: SpoTyping
  • bio.tool description: Fast and accurate + in silico Mycobacterium spoligotyping from sequence reads.
  • EDAM + operation: Variant pattern analysis
  • EDAM topic: + Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic + variation
  • Status: Up-to-date
  • Source: + https://github.com/xiaeryu/SpoTyping-v2.0
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: spotyping
  • Date + of first commit of the suite: 2018-05-07
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping
  • Galaxy + wrapper version: 2.1
  • Conda id: spotyping
  • Conda + version: 2.1
  • EDAM operation (no superclasses): Variant + pattern analysis
  • EDAM topic (no superclasses): Microbiology, + Sequencing, Sequence composition, complexity and repeats, Genetic variation
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 1436
  • No. of tool + users (all time) (usegalaxy.eu): 1436
  • Tool usage (5 years) + (usegalaxy.eu): 23
  • Tool usage (all time) (usegalaxy.eu): + 23
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1436
  • No. + of tool users (all time) - all main servers: 1436
  • Tool + usage (5 years) - all main servers: 23
  • Tool usage (all + time) - all main servers: 23
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: spotyping + - description_md: '
  • Galaxy tool ids: bowtieForSmallRNA
  • Description: + bowtie wrapper tool to align small RNA sequencing reads
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: http://artbio.fr
  • ToolShed + categories: RNA, Next Gen Mappers
  • ToolShed id: sr_bowtie
  • Date + of first commit of the suite: 2017-09-02
  • Galaxy wrapper + owner: artbio
  • Galaxy wrapper source: https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie
  • Galaxy + wrapper parsed folder: https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie
  • Galaxy + wrapper version: 2.3.0
  • Conda id: bowtie
  • Conda + version: 1.3.1
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available 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: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 80
  • No. of tool + users (all time) (usegalaxy.org): 80
  • Tool usage (5 years) + (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): + 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 80
  • No. + of tool users (all time) - all main servers: 80
  • Tool usage + (5 years) - all main servers: 1
  • Tool usage (all time) - + all main servers: 1
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: sr_bowtie + - description_md: '
  • Galaxy tool ids: srst2
  • Description: + Short Read Sequence Typing for Bacterial Pathogens
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: nan
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: srst2
  • Date + of first commit of the suite: 2015-12-02
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: nan
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2
  • Galaxy + wrapper version: 0.3.7
  • Conda id: srst2
  • Conda + version: 0.2.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 297
  • No. of tool + users (all time) (usegalaxy.eu): 297
  • Tool usage (5 years) + (usegalaxy.eu): 40
  • Tool usage (all time) (usegalaxy.eu): + 40
  • No. of tool users (5 years) (usegalaxy.org): 71
  • No. + of tool users (all time) (usegalaxy.org): 71
  • Tool usage + (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): + 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 368
  • No. + of tool users (all time) - all main servers: 368
  • Tool usage + (5 years) - all main servers: 41
  • Tool usage (all time) + - all main servers: 41
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: srst2 + - description_md: '
  • Galaxy tool ids: srst2
  • Description: + SRST2 Short Read Sequence Typing for Bacterial Pathogens
  • bio.tool + id: srst2
  • bio.tool ids: srst2
  • biii: + nan
  • bio.tool name: srst2
  • bio.tool description: + Short Read Sequence Typing for Bacterial Pathogens
  • EDAM operation: + Multilocus sequence typing
  • EDAM topic: Whole genome sequencing, + Public health and epidemiology
  • Status: To update
  • Source: + http://katholt.github.io/srst2/
  • ToolShed categories: Metagenomics
  • ToolShed + id: srst2
  • Date of first commit of the suite: 2022-08-22
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/katholt/srst2
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2
  • Galaxy + wrapper version: 0.2.0
  • Conda id: samtools
  • Conda + version: 1.21
  • EDAM operation (no superclasses): + Multilocus sequence typing
  • EDAM topic (no superclasses): + Whole genome sequencing, Public health and epidemiology
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 297
  • No. of tool + users (all time) (usegalaxy.eu): 297
  • Tool usage (5 years) + (usegalaxy.eu): 40
  • Tool usage (all time) (usegalaxy.eu): + 40
  • No. of tool users (5 years) (usegalaxy.org): 71
  • No. + of tool users (all time) (usegalaxy.org): 71
  • Tool usage + (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): + 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 368
  • No. + of tool users (all time) - all main servers: 368
  • Tool usage + (5 years) - all main servers: 41
  • Tool usage (all time) + - all main servers: 41
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: srst2 + - description_md: '
  • Galaxy tool ids: staramr_search
  • Description: + Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial + resistance databases.
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: + https://github.com/phac-nml/staramr
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: staramr
  • Date + of first commit of the suite: 2022-06-10
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr
  • Galaxy + wrapper version: 0.10.0
  • Conda id: staramr
  • Conda + version: 0.10.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 20778
  • No. of tool + users (all time) (usegalaxy.eu): 20891
  • Tool usage (5 years) + (usegalaxy.eu): 2030
  • Tool usage (all time) (usegalaxy.eu): + 2045
  • No. of tool users (5 years) (usegalaxy.org): 9520
  • No. + of tool users (all time) (usegalaxy.org): 9520
  • Tool usage + (5 years) (usegalaxy.org): 1424
  • Tool usage (all time) (usegalaxy.org): + 1424
  • No. of tool users (5 years) (usegalaxy.org.au): 6753
  • No. + of tool users (all time) (usegalaxy.org.au): 6753
  • Tool + usage (5 years) (usegalaxy.org.au): 864
  • Tool usage (all + time) (usegalaxy.org.au): 864
  • No. of tool users (5 years) + - all main servers: 37051
  • No. of tool users (all time) + - all main servers: 37164
  • Tool usage (5 years) - all main + servers: 4318
  • Tool usage (all time) - all main servers: + 4333
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: staramr + - description_md: '
  • Galaxy tool ids: stringmlst
  • Description: + Rapid and accurate identification of the sequence type (ST)
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: nan
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: stringmlst
  • Date + of first commit of the suite: 2016-10-19
  • Galaxy wrapper + owner: nml
  • Galaxy wrapper source: nan
  • Galaxy + wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst
  • Galaxy + wrapper version: 1.1.0
  • Conda id: stringMLST
  • Conda + version: 0.6.3
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 0
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: stringmlst + - description_md: '
  • Galaxy tool ids: structure
  • Description: + for using multi-locus genotype data to investigate population structure.
  • bio.tool + id: structure
  • bio.tool ids: structure
  • biii: + nan
  • bio.tool name: Structure
  • 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.
  • EDAM + operation: Genetic variation analysis
  • EDAM topic: + Population genetics
  • Status: Up-to-date
  • Source: + https://web.stanford.edu/group/pritchardlab/structure.html
  • ToolShed + categories: Phylogenetics, Variant Analysis
  • ToolShed id: + structure
  • Date of first commit of the suite: 2017-09-22
  • Galaxy + wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure
  • Galaxy + wrapper version: 2.3.4
  • Conda id: structure
  • Conda + version: 2.3.4
  • EDAM operation (no superclasses): + Genetic variation analysis
  • EDAM topic (no superclasses): + Population genetics
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 2858
  • No. of tool users (all time) (usegalaxy.eu): 3001
  • Tool + usage (5 years) (usegalaxy.eu): 118
  • Tool usage (all time) + (usegalaxy.eu): 123
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 2858
  • No. of tool users (all time) - all main + servers: 3001
  • Tool usage (5 years) - all main servers: + 118
  • Tool usage (all time) - all main servers: 123
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: structure + - description_md: '
  • Galaxy tool ids: qiime2__alignment__mafft, + qiime2__alignment__mafft_add, qiime2__alignment__mask
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-alignment
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 3
  • Available + on UseGalaxy.org.au: 3
  • Available on UseGalaxy.eu: + 3
  • Available on UseGalaxy.fr: 3
  • Tools available + on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: + 3
  • Tools available on UseGalaxy.eu: 3
  • Tools + available on UseGalaxy.fr: 3
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 249
  • No. of tool + users (all time) (usegalaxy.eu): 249
  • Tool usage (5 years) + (usegalaxy.eu): 32
  • Tool usage (all time) (usegalaxy.eu): + 32
  • No. of tool users (5 years) (usegalaxy.org): 16
  • No. + of tool users (all time) (usegalaxy.org): 16
  • Tool usage + (5 years) (usegalaxy.org): 10
  • Tool usage (all time) (usegalaxy.org): + 10
  • No. of tool users (5 years) (usegalaxy.org.au): 102
  • No. + of tool users (all time) (usegalaxy.org.au): 102
  • Tool usage + (5 years) (usegalaxy.org.au): 16
  • Tool usage (all time) + (usegalaxy.org.au): 16
  • No. of tool users (5 years) - all + main servers: 367
  • No. of tool users (all time) - all main + servers: 367
  • Tool usage (5 years) - all main servers: + 58
  • Tool usage (all time) - all main servers: 58
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__alignment + - description_md: '
  • Galaxy tool ids: qiime2__composition__add_pseudocount, + qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, + qiime2__composition__tabulate
  • Description: nan
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/qiime2/q2-composition
  • ToolShed + categories: Metagenomics, Sequence Analysis, Statistics
  • ToolShed + id: nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 4
  • Available + on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: + 4
  • Available on UseGalaxy.fr: 2
  • Tools available + on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: + 4
  • Tools available on UseGalaxy.eu: 4
  • Tools + available on UseGalaxy.fr: 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 117
  • No. of tool + users (all time) (usegalaxy.eu): 117
  • Tool usage (5 years) + (usegalaxy.eu): 41
  • Tool usage (all time) (usegalaxy.eu): + 41
  • No. of tool users (5 years) (usegalaxy.org): 84
  • No. + of tool users (all time) (usegalaxy.org): 84
  • Tool usage + (5 years) (usegalaxy.org): 24
  • Tool usage (all time) (usegalaxy.org): + 24
  • No. of tool users (5 years) (usegalaxy.org.au): 161
  • No. + of tool users (all time) (usegalaxy.org.au): 161
  • Tool usage + (5 years) (usegalaxy.org.au): 13
  • Tool usage (all time) + (usegalaxy.org.au): 13
  • No. of tool users (5 years) - all + main servers: 362
  • No. of tool users (all time) - all main + servers: 362
  • Tool usage (5 years) - all main servers: + 78
  • Tool usage (all time) - all main servers: 78
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__composition + - description_md: '
  • Galaxy tool ids: qiime2__cutadapt__demux_paired, + qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-cutadapt
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 4
  • Available + on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: + 4
  • Available on UseGalaxy.fr: 4
  • Tools available + on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: + 4
  • Tools available on UseGalaxy.eu: 4
  • Tools + available on UseGalaxy.fr: 4
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 217
  • No. of tool + users (all time) (usegalaxy.eu): 217
  • Tool usage (5 years) + (usegalaxy.eu): 47
  • Tool usage (all time) (usegalaxy.eu): + 47
  • No. of tool users (5 years) (usegalaxy.org): 42
  • No. + of tool users (all time) (usegalaxy.org): 42
  • Tool usage + (5 years) (usegalaxy.org): 20
  • Tool usage (all time) (usegalaxy.org): + 20
  • No. of tool users (5 years) (usegalaxy.org.au): 96
  • No. + of tool users (all time) (usegalaxy.org.au): 96
  • Tool usage + (5 years) (usegalaxy.org.au): 12
  • Tool usage (all time) + (usegalaxy.org.au): 12
  • No. of tool users (5 years) - all + main servers: 355
  • No. of tool users (all time) - all main + servers: 355
  • Tool usage (5 years) - all main servers: + 79
  • Tool usage (all time) - all main servers: 79
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__cutadapt + - description_md: '
  • Galaxy tool ids: qiime2__dada2__denoise_ccs, + qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + http://benjjneb.github.io/dada2/
  • ToolShed categories: Metagenomics, + Sequence Analysis, Statistics
  • ToolShed id: nan
  • Date + of first commit of the suite: 2022-08-26
  • Galaxy wrapper + owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 4
  • Available + on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: + 4
  • Available on UseGalaxy.fr: 4
  • Tools available + on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: + 4
  • Tools available on UseGalaxy.eu: 4
  • Tools + available on UseGalaxy.fr: 4
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 721
  • No. of tool + users (all time) (usegalaxy.eu): 721
  • Tool usage (5 years) + (usegalaxy.eu): 160
  • Tool usage (all time) (usegalaxy.eu): + 160
  • No. of tool users (5 years) (usegalaxy.org): 350
  • No. + of tool users (all time) (usegalaxy.org): 350
  • Tool usage + (5 years) (usegalaxy.org): 91
  • Tool usage (all time) (usegalaxy.org): + 91
  • No. of tool users (5 years) (usegalaxy.org.au): 214
  • No. + of tool users (all time) (usegalaxy.org.au): 214
  • Tool usage + (5 years) (usegalaxy.org.au): 35
  • Tool usage (all time) + (usegalaxy.org.au): 35
  • No. of tool users (5 years) - all + main servers: 1285
  • No. of tool users (all time) - all main + servers: 1285
  • Tool usage (5 years) - all main servers: + 286
  • Tool usage (all time) - all main servers: 286
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__dada2 + - description_md: '
  • Galaxy tool ids: qiime2__deblur__denoise_16S, + qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/biocore/deblur
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 3
  • Available + on UseGalaxy.org.au: 3
  • Available on UseGalaxy.eu: + 3
  • Available on UseGalaxy.fr: 3
  • Tools available + on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: + 3
  • Tools available on UseGalaxy.eu: 3
  • Tools + available on UseGalaxy.fr: 3
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 125
  • No. of tool + users (all time) (usegalaxy.eu): 125
  • Tool usage (5 years) + (usegalaxy.eu): 30
  • Tool usage (all time) (usegalaxy.eu): + 30
  • No. of tool users (5 years) (usegalaxy.org): 13
  • No. + of tool users (all time) (usegalaxy.org): 13
  • Tool usage + (5 years) (usegalaxy.org): 9
  • Tool usage (all time) (usegalaxy.org): + 9
  • No. of tool users (5 years) (usegalaxy.org.au): 83
  • No. + of tool users (all time) (usegalaxy.org.au): 83
  • Tool usage + (5 years) (usegalaxy.org.au): 8
  • Tool usage (all time) (usegalaxy.org.au): + 8
  • No. of tool users (5 years) - all main servers: 221
  • No. + of tool users (all time) - all main servers: 221
  • Tool usage + (5 years) - all main servers: 47
  • Tool usage (all time) + - all main servers: 47
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: suite_qiime2__deblur + - description_md: '
  • Galaxy tool ids: qiime2__demux__emp_paired, + qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, + qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, + qiime2__demux__summarize, qiime2__demux__tabulate_read_counts
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-demux
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 6
  • Available + on UseGalaxy.org.au: 6
  • Available on UseGalaxy.eu: + 6
  • Available on UseGalaxy.fr: 6
  • Tools available + on UseGalaxy.org (Main): 6
  • Tools available on UseGalaxy.org.au: + 6
  • Tools available on UseGalaxy.eu: 6
  • Tools + available on UseGalaxy.fr: 6
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 396
  • No. of tool + users (all time) (usegalaxy.eu): 396
  • Tool usage (5 years) + (usegalaxy.eu): 134
  • Tool usage (all time) (usegalaxy.eu): + 134
  • No. of tool users (5 years) (usegalaxy.org): 121
  • No. + of tool users (all time) (usegalaxy.org): 121
  • Tool usage + (5 years) (usegalaxy.org): 57
  • Tool usage (all time) (usegalaxy.org): + 57
  • No. of tool users (5 years) (usegalaxy.org.au): 144
  • No. + of tool users (all time) (usegalaxy.org.au): 144
  • Tool usage + (5 years) (usegalaxy.org.au): 39
  • Tool usage (all time) + (usegalaxy.org.au): 39
  • No. of tool users (5 years) - all + main servers: 661
  • No. of tool users (all time) - all main + servers: 661
  • Tool usage (5 years) - all main servers: + 230
  • Tool usage (all time) - all main servers: 230
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__demux + - description_md: '
  • Galaxy tool ids: qiime2__diversity__adonis, + qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, + qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, + qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, + qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, + qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, + qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, + qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, + qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, + qiime2__diversity__umap
  • Description: nan
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/qiime2/q2-diversity
  • ToolShed + categories: Metagenomics, Sequence Analysis, Statistics
  • ToolShed + id: nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 21
  • Available + on UseGalaxy.org.au: 21
  • Available on UseGalaxy.eu: + 22
  • Available on UseGalaxy.fr: 21
  • Tools available + on UseGalaxy.org (Main): 21
  • Tools available on UseGalaxy.org.au: + 21
  • Tools available on UseGalaxy.eu: 22
  • Tools + available on UseGalaxy.fr: 21
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 964
  • No. of tool + users (all time) (usegalaxy.eu): 964
  • Tool usage (5 years) + (usegalaxy.eu): 318
  • Tool usage (all time) (usegalaxy.eu): + 318
  • No. of tool users (5 years) (usegalaxy.org): 249
  • No. + of tool users (all time) (usegalaxy.org): 249
  • Tool usage + (5 years) (usegalaxy.org): 118
  • Tool usage (all time) (usegalaxy.org): + 118
  • No. of tool users (5 years) (usegalaxy.org.au): 475
  • No. + of tool users (all time) (usegalaxy.org.au): 475
  • Tool usage + (5 years) (usegalaxy.org.au): 108
  • Tool usage (all time) + (usegalaxy.org.au): 108
  • No. of tool users (5 years) - all + main servers: 1688
  • No. of tool users (all time) - all main + servers: 1688
  • Tool usage (5 years) - all main servers: + 544
  • Tool usage (all time) - all main servers: 544
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__diversity + - description_md: '
  • Galaxy tool ids: qiime2__diversity_lib__alpha_passthrough, + qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, + qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, + qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, + qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, + qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-diversity-lib
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 12
  • Available + on UseGalaxy.org.au: 12
  • Available on UseGalaxy.eu: + 12
  • Available on UseGalaxy.fr: 12
  • Tools available + on UseGalaxy.org (Main): 12
  • Tools available on UseGalaxy.org.au: + 12
  • Tools available on UseGalaxy.eu: 12
  • Tools + available on UseGalaxy.fr: 12
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 8
  • No. of tool users + (all time) (usegalaxy.eu): 8
  • Tool usage (5 years) (usegalaxy.eu): + 8
  • Tool usage (all time) (usegalaxy.eu): 8
  • No. + of tool users (5 years) (usegalaxy.org): 13
  • No. of tool + users (all time) (usegalaxy.org): 13
  • Tool usage (5 years) + (usegalaxy.org): 11
  • Tool usage (all time) (usegalaxy.org): + 11
  • No. of tool users (5 years) (usegalaxy.org.au): 1302
  • No. + of tool users (all time) (usegalaxy.org.au): 1302
  • Tool + usage (5 years) (usegalaxy.org.au): 19
  • Tool usage (all + time) (usegalaxy.org.au): 19
  • No. of tool users (5 years) + - all main servers: 1323
  • No. of tool users (all time) - + all main servers: 1323
  • Tool usage (5 years) - all main + servers: 38
  • Tool usage (all time) - all main servers: + 38
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: suite_qiime2__diversity_lib + - description_md: '
  • Galaxy tool ids: qiime2__emperor__biplot, + qiime2__emperor__plot, qiime2__emperor__procrustes_plot
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + http://emperor.microbio.me
  • ToolShed categories: Metagenomics, + Sequence Analysis, Statistics
  • ToolShed id: nan
  • Date + of first commit of the suite: 2022-08-26
  • Galaxy wrapper + owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 3
  • Available + on UseGalaxy.org.au: 3
  • Available on UseGalaxy.eu: + 3
  • Available on UseGalaxy.fr: 3
  • Tools available + on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: + 3
  • Tools available on UseGalaxy.eu: 3
  • Tools + available on UseGalaxy.fr: 3
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 58
  • No. of tool + users (all time) (usegalaxy.eu): 58
  • Tool usage (5 years) + (usegalaxy.eu): 23
  • Tool usage (all time) (usegalaxy.eu): + 23
  • No. of tool users (5 years) (usegalaxy.org): 24
  • No. + of tool users (all time) (usegalaxy.org): 24
  • Tool usage + (5 years) (usegalaxy.org): 11
  • Tool usage (all time) (usegalaxy.org): + 11
  • No. of tool users (5 years) (usegalaxy.org.au): 92
  • No. + of tool users (all time) (usegalaxy.org.au): 92
  • Tool usage + (5 years) (usegalaxy.org.au): 11
  • Tool usage (all time) + (usegalaxy.org.au): 11
  • No. of tool users (5 years) - all + main servers: 174
  • No. of tool users (all time) - all main + servers: 174
  • Tool usage (5 years) - all main servers: + 45
  • Tool usage (all time) - all main servers: 45
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__emperor + - description_md: '
  • Galaxy tool ids: qiime2__feature_classifier__blast, + qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, + qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, + qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, + qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, + qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-feature-classifier
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 10
  • Available + on UseGalaxy.org.au: 10
  • Available on UseGalaxy.eu: + 10
  • Available on UseGalaxy.fr: 10
  • Tools available + on UseGalaxy.org (Main): 10
  • Tools available on UseGalaxy.org.au: + 10
  • Tools available on UseGalaxy.eu: 10
  • Tools + available on UseGalaxy.fr: 10
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 863
  • No. of tool + users (all time) (usegalaxy.eu): 863
  • Tool usage (5 years) + (usegalaxy.eu): 220
  • Tool usage (all time) (usegalaxy.eu): + 220
  • No. of tool users (5 years) (usegalaxy.org): 237
  • No. + of tool users (all time) (usegalaxy.org): 237
  • Tool usage + (5 years) (usegalaxy.org): 98
  • Tool usage (all time) (usegalaxy.org): + 98
  • No. of tool users (5 years) (usegalaxy.org.au): 181
  • No. + of tool users (all time) (usegalaxy.org.au): 181
  • Tool usage + (5 years) (usegalaxy.org.au): 41
  • Tool usage (all time) + (usegalaxy.org.au): 41
  • No. of tool users (5 years) - all + main servers: 1281
  • No. of tool users (all time) - all main + servers: 1281
  • Tool usage (5 years) - all main servers: + 359
  • Tool usage (all time) - all main servers: 359
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__feature_classifier + - description_md: '
  • Galaxy tool ids: qiime2__feature_table__core_features, + qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, + qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, + qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, + qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, + qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, + qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, + qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, + qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, + qiime2__feature_table__transpose
  • Description: nan
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/qiime2/q2-feature-table
  • ToolShed + categories: Metagenomics, Sequence Analysis, Statistics
  • ToolShed + id: nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 17
  • Available + on UseGalaxy.org.au: 17
  • Available on UseGalaxy.eu: + 17
  • Available on UseGalaxy.fr: 17
  • Tools available + on UseGalaxy.org (Main): 17
  • Tools available on UseGalaxy.org.au: + 17
  • Tools available on UseGalaxy.eu: 17
  • Tools + available on UseGalaxy.fr: 17
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 983
  • No. of tool + users (all time) (usegalaxy.eu): 983
  • Tool usage (5 years) + (usegalaxy.eu): 287
  • Tool usage (all time) (usegalaxy.eu): + 287
  • No. of tool users (5 years) (usegalaxy.org): 375
  • No. + of tool users (all time) (usegalaxy.org): 375
  • Tool usage + (5 years) (usegalaxy.org): 144
  • Tool usage (all time) (usegalaxy.org): + 144
  • No. of tool users (5 years) (usegalaxy.org.au): 907
  • No. + of tool users (all time) (usegalaxy.org.au): 907
  • Tool usage + (5 years) (usegalaxy.org.au): 106
  • Tool usage (all time) + (usegalaxy.org.au): 106
  • No. of tool users (5 years) - all + main servers: 2265
  • No. of tool users (all time) - all main + servers: 2265
  • Tool usage (5 years) - all main servers: + 537
  • Tool usage (all time) - all main servers: 537
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__feature_table + - description_md: '
  • Galaxy tool ids: qiime2__fragment_insertion__classify_otus_experimental, + qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-fragment-insertion
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 3
  • Available + on UseGalaxy.org.au: 3
  • Available on UseGalaxy.eu: + 3
  • Available on UseGalaxy.fr: 3
  • Tools available + on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: + 3
  • Tools available on UseGalaxy.eu: 3
  • Tools + available on UseGalaxy.fr: 3
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 46
  • No. of tool + users (all time) (usegalaxy.eu): 46
  • Tool usage (5 years) + (usegalaxy.eu): 13
  • Tool usage (all time) (usegalaxy.eu): + 13
  • No. of tool users (5 years) (usegalaxy.org): 9
  • No. + of tool users (all time) (usegalaxy.org): 9
  • Tool usage + (5 years) (usegalaxy.org): 5
  • Tool usage (all time) (usegalaxy.org): + 5
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 55
  • No. + of tool users (all time) - all main servers: 55
  • Tool usage + (5 years) - all main servers: 18
  • Tool usage (all time) + - all main servers: 18
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: suite_qiime2__fragment_insertion + - description_md: '
  • Galaxy tool ids: qiime2__longitudinal__anova, + qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, + qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, + qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, + qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, + qiime2__longitudinal__volatility
  • Description: nan
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/qiime2/q2-longitudinal
  • ToolShed + categories: Metagenomics, Sequence Analysis, Statistics
  • ToolShed + id: nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 11
  • Available + on UseGalaxy.org.au: 11
  • Available on UseGalaxy.eu: + 11
  • Available on UseGalaxy.fr: 11
  • Tools available + on UseGalaxy.org (Main): 11
  • Tools available on UseGalaxy.org.au: + 11
  • Tools available on UseGalaxy.eu: 11
  • Tools + available on UseGalaxy.fr: 11
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 11
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 37
  • No. of tool + users (all time) (usegalaxy.eu): 37
  • Tool usage (5 years) + (usegalaxy.eu): 16
  • Tool usage (all time) (usegalaxy.eu): + 16
  • No. of tool users (5 years) (usegalaxy.org): 22
  • No. + of tool users (all time) (usegalaxy.org): 22
  • Tool usage + (5 years) (usegalaxy.org): 7
  • Tool usage (all time) (usegalaxy.org): + 7
  • No. of tool users (5 years) (usegalaxy.org.au): 89
  • No. + of tool users (all time) (usegalaxy.org.au): 89
  • Tool usage + (5 years) (usegalaxy.org.au): 14
  • Tool usage (all time) + (usegalaxy.org.au): 14
  • No. of tool users (5 years) - all + main servers: 148
  • No. of tool users (all time) - all main + servers: 148
  • Tool usage (5 years) - all main servers: + 37
  • Tool usage (all time) - all main servers: 37
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__longitudinal + - description_md: '
  • Galaxy tool ids: qiime2__metadata__distance_matrix, + qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-metadata
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 3
  • Available + on UseGalaxy.org.au: 3
  • Available on UseGalaxy.eu: + 3
  • Available on UseGalaxy.fr: 3
  • Tools available + on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: + 3
  • Tools available on UseGalaxy.eu: 3
  • Tools + available on UseGalaxy.fr: 3
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 615
  • No. of tool + users (all time) (usegalaxy.eu): 615
  • Tool usage (5 years) + (usegalaxy.eu): 143
  • Tool usage (all time) (usegalaxy.eu): + 143
  • No. of tool users (5 years) (usegalaxy.org): 246
  • No. + of tool users (all time) (usegalaxy.org): 246
  • Tool usage + (5 years) (usegalaxy.org): 75
  • Tool usage (all time) (usegalaxy.org): + 75
  • No. of tool users (5 years) (usegalaxy.org.au): 115
  • No. + of tool users (all time) (usegalaxy.org.au): 115
  • Tool usage + (5 years) (usegalaxy.org.au): 27
  • Tool usage (all time) + (usegalaxy.org.au): 27
  • No. of tool users (5 years) - all + main servers: 976
  • No. of tool users (all time) - all main + servers: 976
  • Tool usage (5 years) - all main servers: + 245
  • Tool usage (all time) - all main servers: 245
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__metadata + - description_md: '
  • Galaxy tool ids: qiime2__phylogeny__align_to_tree_mafft_fasttree, + qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, + qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, + qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, + qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-phylogeny
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 12
  • Available + on UseGalaxy.org.au: 12
  • Available on UseGalaxy.eu: + 12
  • Available on UseGalaxy.fr: 12
  • Tools available + on UseGalaxy.org (Main): 12
  • Tools available on UseGalaxy.org.au: + 12
  • Tools available on UseGalaxy.eu: 12
  • Tools + available on UseGalaxy.fr: 12
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 330
  • No. of tool + users (all time) (usegalaxy.eu): 330
  • Tool usage (5 years) + (usegalaxy.eu): 83
  • Tool usage (all time) (usegalaxy.eu): + 83
  • No. of tool users (5 years) (usegalaxy.org): 64
  • No. + of tool users (all time) (usegalaxy.org): 64
  • Tool usage + (5 years) (usegalaxy.org): 40
  • Tool usage (all time) (usegalaxy.org): + 40
  • No. of tool users (5 years) (usegalaxy.org.au): 195
  • No. + of tool users (all time) (usegalaxy.org.au): 195
  • Tool usage + (5 years) (usegalaxy.org.au): 49
  • Tool usage (all time) + (usegalaxy.org.au): 49
  • No. of tool users (5 years) - all + main servers: 589
  • No. of tool users (all time) - all main + servers: 589
  • Tool usage (5 years) - all main servers: + 172
  • Tool usage (all time) - all main servers: 172
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__phylogeny + - description_md: '
  • Galaxy tool ids: qiime2__quality_control__bowtie2_build, + qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, + qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, + qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, + qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, + qiime2__quality_control__filter_reads
  • Description: nan
  • bio.tool + id: nan
  • bio.tool ids: nan
  • biii: + nan
  • bio.tool name: nan
  • bio.tool description: + nan
  • EDAM operation: nan
  • EDAM topic: + nan
  • Status: To update
  • Source: https://github.com/qiime2/q2-quality-control
  • ToolShed + categories: Metagenomics, Sequence Analysis, Statistics
  • ToolShed + id: nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 6
  • Available + on UseGalaxy.org.au: 6
  • Available on UseGalaxy.eu: + 6
  • Available on UseGalaxy.fr: 6
  • Tools available + on UseGalaxy.org (Main): 6
  • Tools available on UseGalaxy.org.au: + 6
  • Tools available on UseGalaxy.eu: 6
  • Tools + available on UseGalaxy.fr: 6
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 4
  • No. of tool users + (all time) (usegalaxy.eu): 4
  • Tool usage (5 years) (usegalaxy.eu): + 4
  • Tool usage (all time) (usegalaxy.eu): 4
  • No. + of tool users (5 years) (usegalaxy.org): 5
  • No. of tool + users (all time) (usegalaxy.org): 5
  • Tool usage (5 years) + (usegalaxy.org): 5
  • Tool usage (all time) (usegalaxy.org): + 5
  • No. of tool users (5 years) (usegalaxy.org.au): 1
  • No. + of tool users (all time) (usegalaxy.org.au): 1
  • Tool usage + (5 years) (usegalaxy.org.au): 1
  • Tool usage (all time) (usegalaxy.org.au): + 1
  • No. of tool users (5 years) - all main servers: 10
  • No. + of tool users (all time) - all main servers: 10
  • Tool usage + (5 years) - all main servers: 10
  • Tool usage (all time) + - all main servers: 10
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: suite_qiime2__quality_control + - description_md: '
  • Galaxy tool ids: qiime2__quality_filter__q_score
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-quality-filter
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 1
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 1
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 29
  • No. of tool + users (all time) (usegalaxy.eu): 29
  • Tool usage (5 years) + (usegalaxy.eu): 14
  • Tool usage (all time) (usegalaxy.eu): + 14
  • No. of tool users (5 years) (usegalaxy.org): 16
  • No. + of tool users (all time) (usegalaxy.org): 16
  • Tool usage + (5 years) (usegalaxy.org): 6
  • Tool usage (all time) (usegalaxy.org): + 6
  • No. of tool users (5 years) (usegalaxy.org.au): 37
  • No. + of tool users (all time) (usegalaxy.org.au): 37
  • Tool usage + (5 years) (usegalaxy.org.au): 2
  • Tool usage (all time) (usegalaxy.org.au): + 2
  • No. of tool users (5 years) - all main servers: 82
  • No. + of tool users (all time) - all main servers: 82
  • Tool usage + (5 years) - all main servers: 22
  • Tool usage (all time) + - all main servers: 22
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: suite_qiime2__quality_filter + - description_md: '
  • Galaxy tool ids: qiime2__rescript__cull_seqs, + qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, + qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, + qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, + qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, + qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, + qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, + qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, + qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, + qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, + qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/nbokulich/RESCRIPt
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2024-04-25
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 0
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 0
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users + (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): + 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. + of tool users (5 years) (usegalaxy.org): 0
  • No. of tool + users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) + (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 0
  • No. + of tool users (all time) - all main servers: 0
  • Tool usage + (5 years) - all main servers: 0
  • Tool usage (all time) - + all main servers: 0
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: suite_qiime2__rescript + - description_md: '
  • Galaxy tool ids: qiime2__sample_classifier__classify_samples, + qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, + qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, + qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, + qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, + qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, + qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, + qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-sample-classifier
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 15
  • Available + on UseGalaxy.org.au: 15
  • Available on UseGalaxy.eu: + 15
  • Available on UseGalaxy.fr: 15
  • Tools available + on UseGalaxy.org (Main): 15
  • Tools available on UseGalaxy.org.au: + 15
  • Tools available on UseGalaxy.eu: 15
  • Tools + available on UseGalaxy.fr: 15
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 15
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 10
  • No. of tool + users (all time) (usegalaxy.eu): 10
  • Tool usage (5 years) + (usegalaxy.eu): 3
  • Tool usage (all time) (usegalaxy.eu): + 3
  • No. of tool users (5 years) (usegalaxy.org): 14
  • No. + of tool users (all time) (usegalaxy.org): 14
  • Tool usage + (5 years) (usegalaxy.org): 10
  • Tool usage (all time) (usegalaxy.org): + 10
  • No. of tool users (5 years) (usegalaxy.org.au): 5
  • No. + of tool users (all time) (usegalaxy.org.au): 5
  • Tool usage + (5 years) (usegalaxy.org.au): 5
  • Tool usage (all time) (usegalaxy.org.au): + 5
  • No. of tool users (5 years) - all main servers: 29
  • No. + of tool users (all time) - all main servers: 29
  • Tool usage + (5 years) - all main servers: 18
  • Tool usage (all time) + - all main servers: 18
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: suite_qiime2__sample_classifier + - description_md: '
  • Galaxy tool ids: qiime2__taxa__barplot, + qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-taxa
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 4
  • Available + on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: + 4
  • Available on UseGalaxy.fr: 4
  • Tools available + on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: + 4
  • Tools available on UseGalaxy.eu: 4
  • Tools + available on UseGalaxy.fr: 4
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 664
  • No. of tool + users (all time) (usegalaxy.eu): 664
  • Tool usage (5 years) + (usegalaxy.eu): 145
  • Tool usage (all time) (usegalaxy.eu): + 145
  • No. of tool users (5 years) (usegalaxy.org): 113
  • No. + of tool users (all time) (usegalaxy.org): 113
  • Tool usage + (5 years) (usegalaxy.org): 43
  • Tool usage (all time) (usegalaxy.org): + 43
  • No. of tool users (5 years) (usegalaxy.org.au): 255
  • No. + of tool users (all time) (usegalaxy.org.au): 255
  • Tool usage + (5 years) (usegalaxy.org.au): 50
  • Tool usage (all time) + (usegalaxy.org.au): 50
  • No. of tool users (5 years) - all + main servers: 1032
  • No. of tool users (all time) - all main + servers: 1032
  • Tool usage (5 years) - all main servers: + 238
  • Tool usage (all time) - all main servers: 238
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2__taxa + - description_md: '
  • Galaxy tool ids: qiime2__vsearch__cluster_features_closed_reference, + qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, + qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, + qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://github.com/qiime2/q2-vsearch
  • ToolShed categories: + Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: + nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy + wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch
  • Galaxy + wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 8
  • Available + on UseGalaxy.org.au: 8
  • Available on UseGalaxy.eu: + 8
  • Available on UseGalaxy.fr: 7
  • Tools available + on UseGalaxy.org (Main): 8
  • Tools available on UseGalaxy.org.au: + 8
  • Tools available on UseGalaxy.eu: 8
  • Tools + available on UseGalaxy.fr: 7
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 84
  • No. of tool + users (all time) (usegalaxy.eu): 84
  • Tool usage (5 years) + (usegalaxy.eu): 52
  • Tool usage (all time) (usegalaxy.eu): + 52
  • No. of tool users (5 years) (usegalaxy.org): 25
  • No. + of tool users (all time) (usegalaxy.org): 25
  • Tool usage + (5 years) (usegalaxy.org): 16
  • Tool usage (all time) (usegalaxy.org): + 16
  • No. of tool users (5 years) (usegalaxy.org.au): 9
  • No. + of tool users (all time) (usegalaxy.org.au): 9
  • Tool usage + (5 years) (usegalaxy.org.au): 5
  • Tool usage (all time) (usegalaxy.org.au): + 5
  • No. of tool users (5 years) - all main servers: 118
  • No. + of tool users (all time) - all main servers: 118
  • Tool usage + (5 years) - all main servers: 73
  • Tool usage (all time) + - all main servers: 73
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: suite_qiime2__vsearch + - description_md: '
  • Galaxy tool ids: nan
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + nan
  • ToolShed categories: Statistics, Metagenomics, Sequence + Analysis
  • ToolShed id: nan
  • Date of first commit + of the suite: 2022-08-29
  • Galaxy wrapper owner: q2d2
  • Galaxy + wrapper source: nan
  • Galaxy wrapper parsed folder: + https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core
  • Galaxy + wrapper version: nan
  • Conda id: nan
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 0
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 0
  • Tools + available on UseGalaxy.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool + usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) + (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 0
  • No. of tool users (all time) - all main + servers: 0
  • Tool usage (5 years) - all main servers: + 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: suite_qiime2_core + - description_md: '
  • Galaxy tool ids: qiime2_core__tools__export, + qiime2_core__tools__import, qiime2_core__tools__import_fastq
  • Description: + nan
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + https://qiime2.org
  • ToolShed categories: Metagenomics, Sequence + Analysis, Statistics
  • ToolShed id: nan
  • Date + of first commit of the suite: 2022-08-26
  • Galaxy wrapper + owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools
  • Galaxy + wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools
  • Galaxy + wrapper version: 2024.5.0+dist.he540b0b0
  • Conda id: + nan
  • Conda version: nan
  • EDAM operation (no + superclasses): nan
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 2
  • Available + on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: + 2
  • Available on UseGalaxy.fr: 2
  • Tools available + on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: + 2
  • Tools available on UseGalaxy.eu: 2
  • Tools + available on UseGalaxy.fr: 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 14941
  • No. of tool + users (all time) (usegalaxy.eu): 14941
  • Tool usage (5 years) + (usegalaxy.eu): 383
  • Tool usage (all time) (usegalaxy.eu): + 383
  • No. of tool users (5 years) (usegalaxy.org): 25941
  • No. + of tool users (all time) (usegalaxy.org): 25941
  • Tool usage + (5 years) (usegalaxy.org): 255
  • Tool usage (all time) (usegalaxy.org): + 255
  • No. of tool users (5 years) (usegalaxy.org.au): 2856
  • No. + of tool users (all time) (usegalaxy.org.au): 2856
  • Tool + usage (5 years) (usegalaxy.org.au): 112
  • Tool usage (all + time) (usegalaxy.org.au): 112
  • No. of tool users (5 years) + - all main servers: 43738
  • No. of tool users (all time) + - all main servers: 43738
  • Tool usage (5 years) - all main + servers: 750
  • Tool usage (all time) - all main servers: + 750
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: suite_qiime2_core__tools + - description_md: '
  • Galaxy tool ids: Draw_phylogram
  • Description: + Draw phylogeny
  • bio.tool id: t2ps
  • bio.tool + ids: t2ps
  • biii: nan
  • bio.tool name: + Draw phylogeny
  • 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
  • EDAM operation: Phylogenetic tree visualisation
  • EDAM + topic: Phylogenomics
  • Status: To update
  • Source: + https://bitbucket.org/natefoo/taxonomy
  • ToolShed categories: + Metagenomics
  • ToolShed id: t2ps
  • Date of first + commit of the suite: 2014-01-27
  • Galaxy wrapper owner: + devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps
  • Galaxy + wrapper version: 1.0.0
  • Conda id: taxonomy
  • Conda + version: 0.10.0
  • EDAM operation (no superclasses): + Phylogenetic tree visualisation
  • EDAM topic (no superclasses): + Phylogenomics
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 411
  • No. of tool + users (all time) (usegalaxy.eu): 472
  • Tool usage (5 years) + (usegalaxy.eu): 68
  • Tool usage (all time) (usegalaxy.eu): + 90
  • No. of tool users (5 years) (usegalaxy.org): 102
  • No. + of tool users (all time) (usegalaxy.org): 7952
  • Tool usage + (5 years) (usegalaxy.org): 13
  • Tool usage (all time) (usegalaxy.org): + 1240
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 513
  • No. + of tool users (all time) - all main servers: 8424
  • Tool + usage (5 years) - all main servers: 81
  • Tool usage (all + time) - all main servers: 1330
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: t2ps + - description_md: '
  • Galaxy tool ids: t2t_report
  • Description: + Summarize taxonomy
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: To update
  • Source: + https://bitbucket.org/natefoo/taxonomy
  • ToolShed categories: + Metagenomics
  • ToolShed id: t2t_report
  • Date + of first commit of the suite: 2014-01-27
  • Galaxy wrapper + owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report
  • Galaxy + wrapper version: 1.0.0
  • Conda id: taxonomy
  • Conda + version: 0.10.0
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 927
  • No. of tool + users (all time) (usegalaxy.eu): 959
  • Tool usage (5 years) + (usegalaxy.eu): 65
  • Tool usage (all time) (usegalaxy.eu): + 78
  • No. of tool users (5 years) (usegalaxy.org): 130
  • No. + of tool users (all time) (usegalaxy.org): 7194
  • Tool usage + (5 years) (usegalaxy.org): 18
  • Tool usage (all time) (usegalaxy.org): + 1143
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 1057
  • No. + of tool users (all time) - all main servers: 8153
  • Tool + usage (5 years) - all main servers: 83
  • Tool usage (all + time) - all main servers: 1221
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: t2t_report + - description_md: '
  • Galaxy tool ids: t_coffee
  • Description: + T-Coffee
  • bio.tool id: nan
  • bio.tool ids: + nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool + description: nan
  • EDAM operation: nan
  • EDAM + topic: nan
  • Status: To update
  • Source: + http://www.tcoffee.org/
  • ToolShed categories: Sequence Analysis
  • ToolShed + id: t_coffee
  • Date of first commit of the suite: + 2016-12-13
  • Galaxy wrapper owner: earlhaminst
  • Galaxy + wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee
  • Galaxy + wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee
  • Galaxy + wrapper version: 13.45.0.4846264
  • Conda id: t-coffee
  • Conda + version: 13.46.0.919e8c6b
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 3783
  • No. of tool + users (all time) (usegalaxy.eu): 9125
  • Tool usage (5 years) + (usegalaxy.eu): 211
  • Tool usage (all time) (usegalaxy.eu): + 229
  • No. of tool users (5 years) (usegalaxy.org): 1
  • No. + of tool users (all time) (usegalaxy.org): 1
  • Tool usage + (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): + 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 3784
  • No. + of tool users (all time) - all main servers: 9126
  • Tool + usage (5 years) - all main servers: 212
  • Tool usage (all + time) - all main servers: 230
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: t_coffee + - description_md: '
  • Galaxy tool ids: taxonomy_krona_chart
  • Description: + Krona pie chart from taxonomic profile
  • bio.tool id: krona
  • bio.tool + ids: krona
  • biii: nan
  • bio.tool name: + Krona
  • bio.tool description: Krona creates interactive HTML5 + charts of hierarchical data (such as taxonomic abundance in a metagenome).
  • EDAM + operation: Visualisation
  • EDAM topic: Metagenomics
  • Status: + To update
  • Source: http://sourceforge.net/projects/krona/
  • ToolShed + categories: Assembly
  • ToolShed id: taxonomy_krona_chart
  • Date + of first commit of the suite: 2015-08-12
  • Galaxy wrapper + owner: crs4
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart
  • Galaxy + wrapper version: 2.7.1+galaxy0
  • Conda id: krona
  • Conda + version: 2.8.1
  • EDAM operation (no superclasses): + Visualisation
  • EDAM topic (no superclasses): Metagenomics
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 36069
  • No. of tool + users (all time) (usegalaxy.eu): 36922
  • Tool usage (5 years) + (usegalaxy.eu): 5257
  • Tool usage (all time) (usegalaxy.eu): + 5431
  • No. of tool users (5 years) (usegalaxy.org): 25255
  • No. + of tool users (all time) (usegalaxy.org): 30822
  • Tool usage + (5 years) (usegalaxy.org): 5066
  • Tool usage (all time) (usegalaxy.org): + 5826
  • No. of tool users (5 years) (usegalaxy.org.au): 7949
  • No. + of tool users (all time) (usegalaxy.org.au): 7949
  • Tool + usage (5 years) (usegalaxy.org.au): 1584
  • Tool usage (all + time) (usegalaxy.org.au): 1584
  • No. of tool users (5 years) + - all main servers: 69273
  • No. of tool users (all time) + - all main servers: 75693
  • Tool usage (5 years) - all main + servers: 11907
  • Tool usage (all time) - all main servers: + 12841
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: taxonomy_krona_chart + - description_md: '
  • Galaxy tool ids: tb_profiler_profile
  • Description: + Processes M. tuberculosis sequence data to infer strain type and identify known + drug resistance markers.
  • bio.tool id: tb-profiler
  • bio.tool + ids: tb-profiler
  • biii: nan
  • bio.tool + name: tb-profiler
  • bio.tool description: A tool for + drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, + alignments or variants).
  • EDAM operation: Antimicrobial + resistance prediction
  • EDAM topic: nan
  • Status: + To update
  • Source: https://github.com/jodyphelan/TBProfiler
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: tbprofiler
  • Date + of first commit of the suite: 2019-08-16
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler
  • Galaxy + wrapper version: 6.2.1
  • Conda id: tb-profiler
  • Conda + version: 6.3.0
  • EDAM operation (no superclasses): + Antimicrobial resistance prediction
  • EDAM topic (no superclasses): + nan
  • Available on UseGalaxy.org (Main): 1
  • Available + on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: + 1
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 1
  • Tools + available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 6372
  • No. of tool + users (all time) (usegalaxy.eu): 6395
  • Tool usage (5 years) + (usegalaxy.eu): 372
  • Tool usage (all time) (usegalaxy.eu): + 379
  • No. of tool users (5 years) (usegalaxy.org): 7339
  • No. + of tool users (all time) (usegalaxy.org): 7339
  • Tool usage + (5 years) (usegalaxy.org): 378
  • Tool usage (all time) (usegalaxy.org): + 378
  • No. of tool users (5 years) (usegalaxy.org.au): 6966
  • No. + of tool users (all time) (usegalaxy.org.au): 6966
  • Tool + usage (5 years) (usegalaxy.org.au): 154
  • Tool usage (all + time) (usegalaxy.org.au): 154
  • No. of tool users (5 years) + - all main servers: 20677
  • No. of tool users (all time) + - all main servers: 20700
  • Tool usage (5 years) - all main + servers: 904
  • Tool usage (all time) - all main servers: + 911
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: tb-profiler + - description_md: '
  • Galaxy tool ids: tooldistillator, tooldistillator_summarize
  • Description: + ToolDistillator extract and aggregate information from different tool outputs + to JSON parsable files
  • bio.tool id: tooldistillator
  • bio.tool + ids: tooldistillator
  • biii: nan
  • bio.tool + name: ToolDistillator
  • 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.
  • EDAM + operation: Data handling, Parsing
  • EDAM topic: Microbiology, + Bioinformatics, Sequence analysis
  • Status: Up-to-date
  • Source: + https://gitlab.com/ifb-elixirfr/abromics/tooldistillator
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: tooldistillator
  • Date + of first commit of the suite: 2024-04-30
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator
  • Galaxy + wrapper version: 0.9.1
  • Conda id: tooldistillator
  • Conda + version: 0.9.1
  • EDAM operation (no superclasses): + Parsing
  • EDAM topic (no superclasses): Microbiology, Bioinformatics, + Sequence analysis
  • Available on UseGalaxy.org (Main): 2
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 2
  • Available on UseGalaxy.fr: 2
  • Tools available + on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 2
  • Tools + available on UseGalaxy.fr: 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: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 65
  • No. of tool + users (all time) (usegalaxy.eu): 65
  • Tool usage (5 years) + (usegalaxy.eu): 9
  • Tool usage (all time) (usegalaxy.eu): + 9
  • No. of tool users (5 years) (usegalaxy.org): 6
  • No. + of tool users (all time) (usegalaxy.org): 6
  • Tool usage + (5 years) (usegalaxy.org): 5
  • Tool usage (all time) (usegalaxy.org): + 5
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 71
  • No. + of tool users (all time) - all main servers: 71
  • Tool usage + (5 years) - all main servers: 14
  • Tool usage (all time) + - all main servers: 14
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: tooldistillator + - description_md: '
  • Galaxy tool ids: gff_to_prot, transit_gumbel, + transit_hmm, transit_resampling, transit_tn5gaps
  • Description: + TRANSIT
  • bio.tool id: transit
  • bio.tool ids: + transit
  • biii: nan
  • bio.tool name: TRANSIT
  • 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.
  • EDAM operation: Transposon prediction
  • EDAM + topic: DNA, Sequencing, Mobile genetic elements
  • Status: + To update
  • Source: https://github.com/mad-lab/transit/
  • ToolShed + categories: Genome annotation
  • ToolShed id: nan
  • Date + of first commit of the suite: 2019-03-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit
  • Galaxy + wrapper version: 3.0.2
  • Conda id: transit
  • Conda + version: 3.2.3
  • EDAM operation (no superclasses): + Transposon prediction
  • EDAM topic (no superclasses): DNA, + Sequencing, Mobile genetic elements
  • Available on UseGalaxy.org + (Main): 5
  • Available on UseGalaxy.org.au: 5
  • Available + on UseGalaxy.eu: 5
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 5
  • Tools available on + UseGalaxy.org.au: 5
  • Tools available on UseGalaxy.eu: + 5
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools 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.no: 5
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1039
  • No. of tool users (all time) (usegalaxy.eu): 1039
  • Tool + usage (5 years) (usegalaxy.eu): 189
  • Tool usage (all time) + (usegalaxy.eu): 189
  • No. of tool users (5 years) (usegalaxy.org): + 2672
  • No. of tool users (all time) (usegalaxy.org): 3349
  • Tool + usage (5 years) (usegalaxy.org): 467
  • Tool usage (all time) + (usegalaxy.org): 485
  • No. of tool users (5 years) (usegalaxy.org.au): + 358
  • No. of tool users (all time) (usegalaxy.org.au): 358
  • Tool + usage (5 years) (usegalaxy.org.au): 47
  • Tool usage (all + time) (usegalaxy.org.au): 47
  • No. of tool users (5 years) + - all main servers: 4069
  • No. of tool users (all time) - + all main servers: 4746
  • Tool usage (5 years) - all main + servers: 703
  • Tool usage (all time) - all main servers: + 721
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: transit + - description_md: '
  • Galaxy tool ids: transtermhp
  • Description: + Finds rho-independent transcription terminators in bacterial genomes
  • bio.tool + id: transtermhp
  • bio.tool ids: transtermhp
  • biii: + nan
  • bio.tool name: TransTermHP
  • 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
  • EDAM operation: + Transcriptional regulatory element prediction
  • EDAM topic: + Transcription factors and regulatory sites
  • Status: To update
  • Source: + https://transterm.cbcb.umd.edu
  • ToolShed categories: Sequence + Analysis
  • ToolShed id: transtermhp
  • Date of + first commit of the suite: 2015-10-08
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp
  • Galaxy + wrapper version: nan
  • Conda id: transtermhp
  • Conda + version: 2.09
  • EDAM operation (no superclasses): + Transcriptional regulatory element prediction
  • EDAM topic (no superclasses): + Transcription factors and regulatory sites
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 1
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 250
  • No. of tool users (all time) (usegalaxy.eu): 254
  • Tool + usage (5 years) (usegalaxy.eu): 31
  • Tool usage (all time) + (usegalaxy.eu): 31
  • No. of tool users (5 years) (usegalaxy.org): + 174
  • No. of tool users (all time) (usegalaxy.org): 174
  • Tool + usage (5 years) (usegalaxy.org): 45
  • Tool usage (all time) + (usegalaxy.org): 45
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 424
  • No. of tool users (all time) - all main + servers: 428
  • Tool usage (5 years) - all main servers: + 76
  • Tool usage (all time) - all main servers: 76
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: transtermhp + - description_md: '
  • Galaxy tool ids: trim_galore
  • Description: + Trim Galore adaptive quality and adapter trimmer
  • bio.tool id: + trim_galore
  • bio.tool ids: trim_galore
  • biii: + nan
  • bio.tool name: Trim Galore
  • 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.
  • EDAM + operation: Sequence trimming, Primer removal, Read pre-processing
  • EDAM + topic: Sequence analysis
  • Status: To update
  • Source: + http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
  • ToolShed + categories: Sequence Analysis, Fastq Manipulation
  • ToolShed + id: trim_galore
  • Date of first commit of the suite: + 2015-04-22
  • Galaxy wrapper owner: bgruening
  • Galaxy + wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore
  • Galaxy + wrapper version: 0.6.7
  • Conda id: trim-galore
  • Conda + version: 0.6.10
  • EDAM operation (no superclasses): + Sequence trimming, Primer removal, Read pre-processing
  • EDAM topic + (no superclasses): Sequence analysis
  • Available on UseGalaxy.org + (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 229489
  • No. of tool users (all time) (usegalaxy.eu): 275008
  • Tool + usage (5 years) (usegalaxy.eu): 5733
  • Tool usage (all time) + (usegalaxy.eu): 6500
  • No. of tool users (5 years) (usegalaxy.org): + 228708
  • No. of tool users (all time) (usegalaxy.org): 324716
  • Tool + usage (5 years) (usegalaxy.org): 11708
  • Tool usage (all + time) (usegalaxy.org): 16638
  • No. of tool users (5 years) + (usegalaxy.org.au): 22644
  • No. of tool users (all time) + (usegalaxy.org.au): 23869
  • Tool usage (5 years) (usegalaxy.org.au): + 1439
  • Tool usage (all time) (usegalaxy.org.au): 1527
  • No. + of tool users (5 years) - all main servers: 480841
  • No. + of tool users (all time) - all main servers: 623593
  • Tool + usage (5 years) - all main servers: 18880
  • Tool usage (all + time) - all main servers: 24665
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: trim_galore + - description_md: '
  • Galaxy tool ids: trycycler_cluster, trycycler_consensus, + trycycler_partition, trycycler_reconcile_msa, trycycler_subsample
  • Description: + Trycycler toolkit wrappers
  • bio.tool id: nan
  • bio.tool + ids: nan
  • biii: nan
  • bio.tool name: + nan
  • bio.tool description: nan
  • EDAM operation: + nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: + https://github.com/rrwick/Trycycler
  • ToolShed categories: + Assembly
  • ToolShed id: trycycler
  • Date of first + commit of the suite: 2021-02-11
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler
  • Galaxy + wrapper version: 0.5.5
  • Conda id: trycycler
  • Conda + version: 0.5.5
  • EDAM operation (no superclasses): + nan
  • EDAM topic (no superclasses): nan
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 5
  • Available on UseGalaxy.eu: 5
  • Available + on UseGalaxy.fr: 5
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 5
  • Tools + available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: + 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: + 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 14681
  • No. of tool + users (all time) (usegalaxy.eu): 14681
  • Tool usage (5 years) + (usegalaxy.eu): 265
  • Tool usage (all time) (usegalaxy.eu): + 265
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 4488
  • No. + of tool users (all time) (usegalaxy.org.au): 4488
  • Tool + usage (5 years) (usegalaxy.org.au): 147
  • Tool usage (all + time) (usegalaxy.org.au): 147
  • No. of tool users (5 years) + - all main servers: 19169
  • No. of tool users (all time) + - all main servers: 19169
  • Tool usage (5 years) - all main + servers: 412
  • Tool usage (all time) - all main servers: + 412
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: trycycler + - description_md: '
  • Galaxy tool ids: unicycler
  • Description: + Unicycler is a hybrid assembly pipeline for bacterial genomes.
  • bio.tool + id: unicycler
  • bio.tool ids: unicycler
  • biii: + nan
  • bio.tool name: Unicycler
  • bio.tool description: + A tool for assembling bacterial genomes from a combination of short (2nd generation) + and long (3rd generation) sequencing reads.
  • EDAM operation: + Genome assembly, Aggregation
  • EDAM topic: Microbiology, + Genomics, Sequencing, Sequence assembly
  • Status: Up-to-date
  • Source: + https://github.com/rrwick/Unicycler
  • ToolShed categories: + Assembly
  • ToolShed id: unicycler
  • Date of first + commit of the suite: 2018-08-28
  • Galaxy wrapper owner: + iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler
  • Galaxy + wrapper version: 0.5.1
  • Conda id: unicycler
  • Conda + version: 0.5.1
  • EDAM operation (no superclasses): + Genome assembly, Aggregation
  • EDAM topic (no superclasses): + Microbiology, Genomics, Sequencing, Sequence assembly
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 1
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 74120
  • No. of tool + users (all time) (usegalaxy.eu): 77648
  • Tool usage (5 years) + (usegalaxy.eu): 3798
  • Tool usage (all time) (usegalaxy.eu): + 3963
  • No. of tool users (5 years) (usegalaxy.org): 64946
  • No. + of tool users (all time) (usegalaxy.org): 90075
  • Tool usage + (5 years) (usegalaxy.org): 5451
  • Tool usage (all time) (usegalaxy.org): + 7380
  • No. of tool users (5 years) (usegalaxy.org.au): 19516
  • No. + of tool users (all time) (usegalaxy.org.au): 20422
  • Tool + usage (5 years) (usegalaxy.org.au): 2010
  • Tool usage (all + time) (usegalaxy.org.au): 2080
  • No. of tool users (5 years) + - all main servers: 158582
  • No. of tool users (all time) + - all main servers: 188145
  • Tool usage (5 years) - all main + servers: 11259
  • Tool usage (all time) - all main servers: + 13423
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: unicycler + - description_md: '
  • Galaxy tool ids: unipept
  • Description: + Unipept retrieves metaproteomics information
  • bio.tool id: + unipept
  • bio.tool ids: unipept
  • biii: + nan
  • bio.tool name: Unipept
  • bio.tool description: + Metaproteomics data analysis with a focus on interactive data visualizations.
  • EDAM + operation: Prediction and recognition, Visualisation
  • EDAM + topic: Proteomics, Proteogenomics, Biodiversity, Workflows
  • Status: + To update
  • Source: https://github.com/galaxyproteomics/tools-galaxyp
  • ToolShed + categories: Proteomics
  • ToolShed id: unipept
  • Date + of first commit of the suite: 2015-04-03
  • Galaxy wrapper + owner: galaxyp
  • Galaxy wrapper source: https://unipept.ugent.be/apidocs
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept
  • Galaxy + wrapper version: 4.5.1
  • Conda id: python
  • Conda + version: nan
  • EDAM operation (no superclasses): Prediction + and recognition, Visualisation
  • EDAM topic (no superclasses): + Proteomics, Proteogenomics, Biodiversity, Workflows
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 4900
  • No. of tool + users (all time) (usegalaxy.eu): 5146
  • Tool usage (5 years) + (usegalaxy.eu): 257
  • Tool usage (all time) (usegalaxy.eu): + 270
  • No. of tool users (5 years) (usegalaxy.org): 251
  • No. + of tool users (all time) (usegalaxy.org): 251
  • Tool usage + (5 years) (usegalaxy.org): 81
  • Tool usage (all time) (usegalaxy.org): + 81
  • No. of tool users (5 years) (usegalaxy.org.au): 1069
  • No. + of tool users (all time) (usegalaxy.org.au): 1069
  • Tool + usage (5 years) (usegalaxy.org.au): 29
  • Tool usage (all + time) (usegalaxy.org.au): 29
  • No. of tool users (5 years) + - all main servers: 6220
  • No. of tool users (all time) - + all main servers: 6466
  • Tool usage (5 years) - all main + servers: 367
  • Tool usage (all time) - all main servers: + 380
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: unipept + - description_md: '
  • Galaxy tool ids: uniprotxml_downloader
  • Description: + Download UniProt proteome in XML or fasta format
  • bio.tool id: + nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool + name: nan
  • bio.tool description: nan
  • EDAM + operation: nan
  • EDAM topic: nan
  • Status: + To update
  • Source: nan
  • ToolShed categories: + Proteomics
  • ToolShed id: uniprotxml_downloader
  • Date + of first commit of the suite: 2016-03-08
  • Galaxy wrapper + owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader
  • Galaxy + wrapper version: 2.4.0
  • Conda id: requests
  • Conda + version: nan
  • EDAM operation (no superclasses): nan
  • EDAM + topic (no superclasses): nan
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 1
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools + available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: + 0
  • Tools available on UseGalaxy.cz: 1
  • Tools + available on UseGalaxy.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1488
  • No. of tool users (all time) (usegalaxy.eu): 1596
  • Tool + usage (5 years) (usegalaxy.eu): 230
  • Tool usage (all time) + (usegalaxy.eu): 266
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 743
  • No. of tool users (all time) (usegalaxy.org.au): 743
  • Tool + usage (5 years) (usegalaxy.org.au): 35
  • Tool usage (all + time) (usegalaxy.org.au): 35
  • No. of tool users (5 years) + - all main servers: 2231
  • No. of tool users (all time) - + all main servers: 2339
  • Tool usage (5 years) - all main + servers: 265
  • Tool usage (all time) - all main servers: + 301
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: uniprotxml_downloader + - description_md: '
  • Galaxy tool ids: usher_matutils, usher
  • Description: + UShER toolkit wrappers
  • bio.tool id: usher
  • bio.tool + ids: usher
  • biii: nan
  • bio.tool name: + usher
  • 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.
  • EDAM + operation: Classification, Phylogenetic tree visualisation, Phylogenetic + inference (from molecular sequences)
  • EDAM topic: Phylogeny, + Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics
  • Status: + To update
  • Source: https://github.com/yatisht/usher
  • ToolShed + categories: Phylogenetics
  • ToolShed id: usher
  • Date + of first commit of the suite: 2021-05-11
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher
  • Galaxy + wrapper version: 0.2.1
  • Conda id: usher
  • Conda + version: 0.6.3
  • EDAM operation (no superclasses): + Classification, Phylogenetic tree visualisation, Phylogenetic inference (from + molecular sequences)
  • EDAM topic (no superclasses): Cladistics, + Genotype and phenotype, Phylogenomics
  • Available on UseGalaxy.org + (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 2
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available on Dintor: + 0
  • Tools available on GASLINI: 0
  • Tools available + on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: + 0
  • Tools available on GalaxyTrakr: 0
  • Tools + available on Genomic Hyperbrowser: 0
  • Tools available on + GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: + 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools + available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: + 0
  • Tools available on MISSISSIPPI: 0
  • Tools + available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: + 0
  • Tools available on Oqtans: 0
  • Tools available + 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.no: 0
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1060
  • No. of tool users (all time) (usegalaxy.eu): 1060
  • Tool + usage (5 years) (usegalaxy.eu): 5
  • Tool usage (all time) + (usegalaxy.eu): 5
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 1060
  • No. of tool users (all time) - all main + servers: 1060
  • Tool usage (5 years) - all main servers: + 5
  • Tool usage (all time) - all main servers: 5
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: usher + - description_md: '
  • Galaxy tool ids: valet
  • Description: + A pipeline for detecting mis-assemblies in metagenomic assemblies.
  • bio.tool + id: valet
  • bio.tool ids: valet
  • biii: + nan
  • bio.tool name: VALET
  • bio.tool description: + VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.
  • EDAM + operation: Sequence assembly, Sequence assembly visualisation
  • EDAM + topic: Metagenomics, Sequence assembly
  • Status: To + update
  • Source: https://github.com/marbl/VALET
  • ToolShed + categories: Metagenomics
  • ToolShed id: valet
  • Date + of first commit of the suite: 2017-11-16
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet
  • Galaxy + wrapper version: nan
  • Conda id: valet
  • Conda + version: 1.0
  • EDAM operation (no superclasses): Sequence + assembly, Sequence assembly visualisation
  • EDAM topic (no superclasses): + Metagenomics, Sequence assembly
  • Available on UseGalaxy.org (Main): + 1
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 1
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 518
  • No. of tool users (all time) (usegalaxy.eu): 677
  • Tool + usage (5 years) (usegalaxy.eu): 75
  • Tool usage (all time) + (usegalaxy.eu): 87
  • No. of tool users (5 years) (usegalaxy.org): + 234
  • No. of tool users (all time) (usegalaxy.org): 234
  • Tool + usage (5 years) (usegalaxy.org): 65
  • Tool usage (all time) + (usegalaxy.org): 65
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 752
  • No. of tool users (all time) - all main + servers: 911
  • Tool usage (5 years) - all main servers: + 140
  • Tool usage (all time) - all main servers: 152
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: valet + - description_md: '
  • Galaxy tool ids: vapor
  • Description: + Classify Influenza samples from raw short read sequence data
  • bio.tool + id: vapor
  • bio.tool ids: vapor
  • biii: + nan
  • bio.tool name: VAPOR
  • 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.
  • EDAM operation: Data retrieval, De-novo assembly, + Read mapping
  • EDAM topic: Whole genome sequencing, Mapping, + Sequence assembly
  • Status: Up-to-date
  • Source: + https://github.com/connor-lab/vapor
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: vapor
  • Date + of first commit of the suite: 2022-08-24
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor
  • Galaxy + wrapper version: 1.0.2
  • Conda id: vapor
  • Conda + version: 1.0.2
  • EDAM operation (no superclasses): + Data retrieval, De-novo assembly, Read mapping
  • EDAM topic (no + superclasses): Whole genome sequencing, Mapping, Sequence assembly
  • Available + on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 5936
  • No. of tool + users (all time) (usegalaxy.eu): 5936
  • Tool usage (5 years) + (usegalaxy.eu): 147
  • Tool usage (all time) (usegalaxy.eu): + 147
  • No. of tool users (5 years) (usegalaxy.org): 523
  • No. + of tool users (all time) (usegalaxy.org): 523
  • Tool usage + (5 years) (usegalaxy.org): 15
  • Tool usage (all time) (usegalaxy.org): + 15
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 6459
  • No. + of tool users (all time) - all main servers: 6459
  • Tool + usage (5 years) - all main servers: 162
  • Tool usage (all + time) - all main servers: 162
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: vapor + - description_md: '
  • Galaxy tool ids: varvamp
  • Description: + Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse + viruses
  • bio.tool id: varvamp
  • bio.tool ids: + varvamp
  • biii: nan
  • bio.tool name: varVAMP
  • 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.
  • EDAM operation: PCR primer design
  • EDAM + topic: Virology, Probes and primers
  • Status: To update
  • Source: + https://github.com/jonas-fuchs/varVAMP/
  • ToolShed categories: + Sequence Analysis
  • ToolShed id: varvamp
  • Date + of first commit of the suite: 2024-01-27
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/jonas-fuchs/varVAMP
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp
  • Galaxy + wrapper version: 1.2.0
  • Conda id: varvamp
  • Conda + version: 1.2.1
  • EDAM operation (no superclasses): + PCR primer design
  • EDAM topic (no superclasses): Virology, + Probes and primers
  • Available on UseGalaxy.org (Main): 0
  • Available + on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: + 1
  • Available on UseGalaxy.fr: 0
  • Tools available + on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: + 0
  • Tools available on UseGalaxy.eu: 1
  • Tools + available on UseGalaxy.fr: 0
  • Tools available on APOSTL: + 0
  • Tools available on ARGs-OAP: 0
  • Tools available + on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools + available on Coloc-stats: 0
  • Tools available on CropGalaxy: + 0
  • Tools available on Dintor: 0
  • Tools available + on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 273
  • No. of tool + users (all time) (usegalaxy.eu): 273
  • Tool usage (5 years) + (usegalaxy.eu): 12
  • Tool usage (all time) (usegalaxy.eu): + 12
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 273
  • No. + of tool users (all time) - all main servers: 273
  • Tool usage + (5 years) - all main servers: 12
  • Tool usage (all time) + - all main servers: 12
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: varvamp + - description_md: '
  • Galaxy tool ids: vegan_diversity, vegan_fisher_alpha, + vegan_rarefaction
  • Description: an R package fo community + ecologist
  • bio.tool id: vegan
  • bio.tool ids: + vegan
  • biii: nan
  • bio.tool name: vegan
  • bio.tool + description: Ordination methods, diversity analysis and other functions + for community and vegetation ecologists
  • EDAM operation: + Standardisation and normalisation, Analysis
  • EDAM topic: + Ecology, Phylogenetics, Environmental science
  • Status: To + update
  • Source: https://cran.r-project.org/package=vegan
  • ToolShed + categories: Metagenomics
  • ToolShed id: nan
  • Date + of first commit of the suite: 2015-08-27
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan
  • Galaxy + wrapper version: 2.4-3
  • Conda id: r-vegan
  • Conda + version: 2.3_4
  • EDAM operation (no superclasses): + Standardisation and normalisation, Analysis
  • EDAM topic (no superclasses): + Ecology, Phylogenetics, Environmental science
  • Available on UseGalaxy.org + (Main): 3
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 3
  • Available on UseGalaxy.fr: 0
  • Tools + available on UseGalaxy.org (Main): 3
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 3
  • Tools available on UseGalaxy.fr: 0
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 2157
  • No. of tool users (all time) (usegalaxy.eu): 2287
  • Tool + usage (5 years) (usegalaxy.eu): 198
  • Tool usage (all time) + (usegalaxy.eu): 209
  • No. of tool users (5 years) (usegalaxy.org): + 3930
  • No. of tool users (all time) (usegalaxy.org): 5591
  • Tool + usage (5 years) (usegalaxy.org): 446
  • Tool usage (all time) + (usegalaxy.org): 744
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 6087
  • No. of tool users (all time) - all main + servers: 7878
  • Tool usage (5 years) - all main servers: + 644
  • Tool usage (all time) - all main servers: 953
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: vegan + - description_md: '
  • Galaxy tool ids: velvetg, velveth
  • Description: + de novo genomic assembler specially designed for short read sequencing technologies
  • bio.tool + id: velvet
  • bio.tool ids: velvet
  • biii: + nan
  • bio.tool name: Velvet
  • bio.tool description: + A de novo genomic assembler specially designed for short read sequencing technologies, + such as Solexa or 454 or SOLiD.
  • EDAM operation: Formatting, + De-novo assembly
  • EDAM topic: Sequence assembly
  • Status: + To update
  • Source: https://www.ebi.ac.uk/~zerbino/velvet/
  • ToolShed + categories: Assembly
  • ToolShed id: velvet
  • Date + of first commit of the suite: 2020-06-09
  • Galaxy wrapper + owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet
  • Galaxy + wrapper version: nan
  • Conda id: velvet
  • Conda + version: 1.2.10
  • EDAM operation (no superclasses): + Formatting, De-novo assembly
  • EDAM topic (no superclasses): + Sequence assembly
  • Available on UseGalaxy.org (Main): 2
  • Available + on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: + 2
  • Available on UseGalaxy.fr: 2
  • Tools available + on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: + 2
  • Tools available on UseGalaxy.eu: 2
  • Tools + available on UseGalaxy.fr: 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: 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.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 25171
  • No. of tool + users (all time) (usegalaxy.eu): 27943
  • Tool usage (5 years) + (usegalaxy.eu): 3899
  • Tool usage (all time) (usegalaxy.eu): + 4270
  • No. of tool users (5 years) (usegalaxy.org): 51187
  • No. + of tool users (all time) (usegalaxy.org): 51187
  • Tool usage + (5 years) (usegalaxy.org): 7557
  • Tool usage (all time) (usegalaxy.org): + 7557
  • No. of tool users (5 years) (usegalaxy.org.au): 28546
  • No. + of tool users (all time) (usegalaxy.org.au): 28619
  • Tool + usage (5 years) (usegalaxy.org.au): 3585
  • Tool usage (all + time) (usegalaxy.org.au): 3613
  • No. of tool users (5 years) + - all main servers: 104904
  • No. of tool users (all time) + - all main servers: 107749
  • Tool usage (5 years) - all main + servers: 15041
  • Tool usage (all time) - all main servers: + 15440
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: velvet + - description_md: '
  • Galaxy tool ids: velvetoptimiser
  • Description: + Automatically optimize Velvet assemblies
  • bio.tool id: velvetoptimiser
  • bio.tool + ids: velvetoptimiser
  • biii: nan
  • bio.tool + name: VelvetOptimiser
  • 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.
  • EDAM + operation: Optimisation and refinement, Sequence assembly
  • EDAM + topic: Genomics, Sequence assembly
  • Status: To update
  • Source: + nan
  • ToolShed categories: Assembly
  • ToolShed + id: velvetoptimiser
  • Date of first commit of the suite: + 2017-12-19
  • Galaxy wrapper owner: simon-gladman
  • Galaxy + wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser
  • Galaxy + wrapper version: 2.2.6+galaxy2
  • Conda id: velvet
  • Conda + version: 1.2.10
  • EDAM operation (no superclasses): + Optimisation and refinement, Sequence assembly
  • EDAM topic (no + superclasses): Genomics, Sequence assembly
  • Available on + UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: + 1
  • Available on UseGalaxy.eu: 1
  • Available + on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): + 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools + available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: + 0
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available 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.no: + 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 4715
  • No. of tool + users (all time) (usegalaxy.eu): 5343
  • Tool usage (5 years) + (usegalaxy.eu): 888
  • Tool usage (all time) (usegalaxy.eu): + 965
  • No. of tool users (5 years) (usegalaxy.org): 9575
  • No. + of tool users (all time) (usegalaxy.org): 9576
  • Tool usage + (5 years) (usegalaxy.org): 2117
  • Tool usage (all time) (usegalaxy.org): + 2117
  • No. of tool users (5 years) (usegalaxy.org.au): 3271
  • No. + of tool users (all time) (usegalaxy.org.au): 5524
  • Tool + usage (5 years) (usegalaxy.org.au): 1050
  • Tool usage (all + time) (usegalaxy.org.au): 1397
  • No. of tool users (5 years) + - all main servers: 17561
  • No. of tool users (all time) + - all main servers: 20443
  • Tool usage (5 years) - all main + servers: 4055
  • Tool usage (all time) - all main servers: + 4479
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: velvet_optimiser + - description_md: '
  • Galaxy tool ids: virannot_blast2tsv, virannot_otu, + virAnnot_rps2tsv
  • Description: virAnnot wrappers
  • bio.tool + id: virannot
  • bio.tool ids: virannot
  • biii: + nan
  • bio.tool name: virAnnot
  • 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.
  • EDAM operation: Sequence + annotation, Sequence clustering, Sequence cluster visualisation
  • EDAM + topic: Metagenomics, Virology, Microbial ecology
  • Status: + To update
  • Source: https://github.com/marieBvr/virAnnot
  • ToolShed + categories: Metagenomics
  • ToolShed id: virannot
  • Date + of first commit of the suite: 2024-03-04
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot
  • Galaxy + wrapper version: 1.1.0+galaxy0
  • Conda id: biopython
  • Conda + version: 1.70
  • EDAM operation (no superclasses): + Sequence annotation, Sequence clustering, Sequence cluster visualisation
  • EDAM + topic (no superclasses): Metagenomics, Virology, Microbial ecology
  • Available + on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: + 0
  • Available on UseGalaxy.eu: 3
  • Available + on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): + 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools + available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: + 3
  • Tools available on APOSTL: 0
  • Tools available + on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools + available on ChemFlow: 0
  • Tools available on Coloc-stats: + 0
  • Tools available on CropGalaxy: 0
  • Tools + available on Dintor: 0
  • Tools available on GASLINI: + 0
  • Tools available on Galaxy@AuBi: 0
  • Tools + available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: + 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools + available on GigaGalaxy: 0
  • Tools available on HyPhy HIV + NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: + 0
  • Tools available on ImmPort Galaxy: 0
  • Tools + available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: + 0
  • Tools available on Mandoiu Lab: 0
  • Tools + available on MiModD NacreousMap: 0
  • Tools available on Oqtans: + 0
  • Tools available on Palfinder: 0
  • Tools available + on PepSimili: 0
  • Tools available on PhagePromotor: + 0
  • Tools available on UseGalaxy.be: 0
  • Tools + available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: + 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. + of tool users (5 years) (usegalaxy.eu): 94
  • No. of tool + users (all time) (usegalaxy.eu): 94
  • Tool usage (5 years) + (usegalaxy.eu): 16
  • Tool usage (all time) (usegalaxy.eu): + 16
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. + of tool users (all time) (usegalaxy.org): 0
  • Tool usage + (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): + 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. + of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage + (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): + 0
  • No. of tool users (5 years) - all main servers: 94
  • No. + of tool users (all time) - all main servers: 94
  • Tool usage + (5 years) - all main servers: 16
  • Tool usage (all time) + - all main servers: 16
  • Reviewed: True
  • To + keep: True
  • Deprecated: False
' + title_md: virAnnot + - description_md: '
  • Galaxy tool ids: vsearch_alignment, vsearch_chimera_detection, + vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, + vsearch_shuffling, vsearch_sorting
  • Description: VSEARCH + including searching, clustering, chimera detection, dereplication, sorting, + masking and shuffling of sequences.
  • bio.tool id: vsearch
  • bio.tool + ids: vsearch
  • biii: nan
  • bio.tool name: + VSEARCH
  • 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.
  • EDAM operation: DNA mapping, Chimera detection
  • EDAM + topic: Metagenomics, Sequence analysis
  • Status: To + update
  • Source: https://github.com/torognes/vsearch
  • ToolShed + categories: Sequence Analysis
  • ToolShed id: vsearch
  • Date + of first commit of the suite: 2015-07-01
  • Galaxy wrapper + owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch
  • Galaxy + wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch
  • Galaxy + wrapper version: 2.8.3
  • Conda id: vsearch
  • Conda + version: 2.29.0
  • EDAM operation (no superclasses): + DNA mapping, Chimera detection
  • EDAM topic (no superclasses): + Metagenomics, Sequence analysis
  • Available on UseGalaxy.org (Main): + 8
  • Available on UseGalaxy.org.au: 8
  • Available + on UseGalaxy.eu: 8
  • Available on UseGalaxy.fr: 8
  • Tools + available on UseGalaxy.org (Main): 8
  • Tools available on + UseGalaxy.org.au: 8
  • Tools available on UseGalaxy.eu: + 8
  • Tools available on UseGalaxy.fr: 8
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available 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.no: 8
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 9694
  • No. of tool users (all time) (usegalaxy.eu): 10338
  • Tool + usage (5 years) (usegalaxy.eu): 559
  • Tool usage (all time) + (usegalaxy.eu): 628
  • No. of tool users (5 years) (usegalaxy.org): + 12282
  • No. of tool users (all time) (usegalaxy.org): 53546
  • Tool + usage (5 years) (usegalaxy.org): 1031
  • Tool usage (all time) + (usegalaxy.org): 2007
  • No. of tool users (5 years) (usegalaxy.org.au): + 5334
  • No. of tool users (all time) (usegalaxy.org.au): 5672
  • Tool + usage (5 years) (usegalaxy.org.au): 246
  • Tool usage (all + time) (usegalaxy.org.au): 277
  • No. of tool users (5 years) + - all main servers: 27310
  • No. of tool users (all time) + - all main servers: 69556
  • Tool usage (5 years) - all main + servers: 1836
  • Tool usage (all time) - all main servers: + 2912
  • Reviewed: True
  • To keep: True
  • Deprecated: + False
' + title_md: vsearch + - description_md: '
  • Galaxy tool ids: wtdbg
  • Description: + WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.
  • bio.tool + id: wtdbg2
  • bio.tool ids: wtdbg2
  • biii: + nan
  • bio.tool name: wtdbg2
  • 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.
  • EDAM operation: Genome assembly, De-novo + assembly
  • EDAM topic: Sequence assembly, Sequencing
  • Status: + Up-to-date
  • Source: https://github.com/ruanjue/wtdbg2
  • ToolShed + categories: Assembly
  • ToolShed id: wtdbg
  • Date + of first commit of the suite: 2018-06-12
  • Galaxy wrapper + owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg
  • Galaxy + wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg
  • Galaxy + wrapper version: 2.5
  • Conda id: wtdbg
  • Conda + version: 2.5
  • EDAM operation (no superclasses): Genome + assembly, De-novo assembly
  • EDAM topic (no superclasses): + Sequence assembly, Sequencing
  • Available on UseGalaxy.org (Main): + 0
  • Available on UseGalaxy.org.au: 0
  • Available + on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools + available on UseGalaxy.org (Main): 0
  • Tools available on + UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: + 1
  • Tools available on UseGalaxy.fr: 1
  • Tools + available on APOSTL: 0
  • Tools available on ARGs-OAP: + 0
  • Tools available on CIRM-CFBP: 0
  • Tools available + on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools + available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant + Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): + 1619
  • No. of tool users (all time) (usegalaxy.eu): 1715
  • Tool + usage (5 years) (usegalaxy.eu): 337
  • Tool usage (all time) + (usegalaxy.eu): 376
  • No. of tool users (5 years) (usegalaxy.org): + 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool + usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) + (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): + 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool + usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) + (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all + main servers: 1619
  • No. of tool users (all time) - all main + servers: 1715
  • Tool usage (5 years) - all main servers: + 337
  • Tool usage (all time) - all main servers: 376
  • Reviewed: + True
  • To keep: True
  • Deprecated: False
' + title_md: wtdbg + id: tool_list + title: List of community curated tools available for microGalaxy +title: Community Tools From 8dc2d4fe12da01d82d649c55daa8d9fcb8d2673c Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 16:18:55 +0100 Subject: [PATCH 12/38] multiple tools --- .../microgalaxy/lab/sections/5_tools.yml | 16557 +--------------- 1 file changed, 450 insertions(+), 16107 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 31f1980c..77e11abf 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -1,16400 +1,743 @@ id: tools tabs: - content: - - description_md: '
  • Galaxy tool ids: pampa_communitymetrics, - pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm
  • Description: - Tools to compute and analyse biodiversity metrics
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: nan
  • ToolShed categories: - Ecology
  • ToolShed id: pampa
  • Date of first - commit of the suite: 2020-11-13
  • Galaxy wrapper owner: - ecology
  • Galaxy wrapper source: https://github.com/ColineRoyaux/PAMPA-Galaxy
  • Galaxy - wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA
  • Galaxy - wrapper version: 0.0.2
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 5
  • Available - on UseGalaxy.eu: 5
  • Available on UseGalaxy.fr: 5
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 5
  • Tools available on UseGalaxy.eu: - 5
  • Tools available on UseGalaxy.fr: 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: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - 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.no: 4
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1038
  • No. of tool users (all time) (usegalaxy.eu): 1038
  • Tool - usage (5 years) (usegalaxy.eu): 146
  • Tool usage (all time) - (usegalaxy.eu): 146
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 849
  • No. of tool users (all time) (usegalaxy.org.au): 849
  • Tool - usage (5 years) (usegalaxy.org.au): 38
  • Tool usage (all - time) (usegalaxy.org.au): 38
  • No. of tool users (5 years) - - all main servers: 1887
  • No. of tool users (all time) - - all main servers: 1887
  • Tool usage (5 years) - all main - servers: 184
  • Tool usage (all time) - all main servers: - 184
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Tools to compute and analyse biodiversity metrics title_md: PAMPA - - description_md: '
  • Galaxy tool ids: treebest_best
  • Description: - TreeBeST best
  • bio.tool id: treebest
  • bio.tool - ids: treebest
  • biii: nan
  • bio.tool name: - TreeBeST
  • 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.
  • EDAM - operation: Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic - inference (from molecular sequences)
  • EDAM topic: Phylogenetics
  • Status: - To update
  • Source: http://treesoft.sourceforge.net/treebest.shtml
  • ToolShed - categories: Phylogenetics
  • ToolShed id: treebest_best
  • Date - of first commit of the suite: 2015-08-06
  • Galaxy wrapper - owner: earlhaminst
  • Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest
  • Galaxy - wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest
  • Galaxy - wrapper version: 1.9.2.post0
  • Conda id: treebest
  • Conda - version: 1.9.2.post1
  • EDAM operation (no superclasses): - Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)
  • EDAM - topic (no superclasses): Phylogenetics
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1003
  • No. of tool users (all time) (usegalaxy.eu): 1022
  • Tool - usage (5 years) (usegalaxy.eu): 48
  • Tool usage (all time) - (usegalaxy.eu): 52
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 1003
  • No. of tool users (all time) - all main - servers: 1022
  • Tool usage (5 years) - all main servers: - 48
  • Tool usage (all time) - all main servers: 52
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: TreeBeST best title_md: TreeBest - - description_md: '
  • Galaxy tool ids: abacas
  • Description: - Order and Orientate Contigs
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://github.com/phac-nml/abacas
  • ToolShed categories: - Assembly
  • ToolShed id: abacas
  • Date of first - commit of the suite: 2019-11-20
  • Galaxy wrapper owner: - nml
  • Galaxy wrapper source: https://github.com/phac-nml/abacas
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas
  • Galaxy - wrapper version: 1.1
  • Conda id: mummer
  • Conda - version: 3.23
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Order and Orientate Contigs title_md: abacas - - description_md: '
  • Galaxy tool ids: abricate, abricate_list, - abricate_summary
  • Description: Mass screening of contigs - for antiobiotic resistance genes
  • bio.tool id: ABRicate
  • bio.tool - ids: ABRicate
  • biii: nan
  • bio.tool name: - ABRicate
  • bio.tool description: Mass screening of contigs - for antimicrobial resistance or virulence genes.
  • EDAM operation: - Antimicrobial resistance prediction
  • EDAM topic: Genomics, - Microbiology
  • Status: Up-to-date
  • Source: - https://github.com/tseemann/abricate
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: abricate
  • Date - of first commit of the suite: 2017-07-10
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate
  • Galaxy - wrapper version: 1.0.1
  • Conda id: abricate
  • Conda - version: 1.0.1
  • EDAM operation (no superclasses): - Antimicrobial resistance prediction
  • EDAM topic (no superclasses): - Genomics, Microbiology
  • Available on UseGalaxy.org (Main): - 3
  • Available on UseGalaxy.org.au: 3
  • Available - on UseGalaxy.eu: 3
  • Available on UseGalaxy.fr: 3
  • Tools - available on UseGalaxy.org (Main): 3
  • Tools available on - UseGalaxy.org.au: 3
  • Tools available on UseGalaxy.eu: - 3
  • Tools available on UseGalaxy.fr: 3
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 619817
  • No. of tool users (all time) (usegalaxy.eu): 622353
  • Tool - usage (5 years) (usegalaxy.eu): 4097
  • Tool usage (all time) - (usegalaxy.eu): 4130
  • No. of tool users (5 years) (usegalaxy.org): - 320454
  • No. of tool users (all time) (usegalaxy.org): 320454
  • Tool - usage (5 years) (usegalaxy.org): 2915
  • Tool usage (all time) - (usegalaxy.org): 2915
  • No. of tool users (5 years) (usegalaxy.org.au): - 496156
  • No. of tool users (all time) (usegalaxy.org.au): - 503743
  • Tool usage (5 years) (usegalaxy.org.au): 2012
  • Tool - usage (all time) (usegalaxy.org.au): 2227
  • No. of tool users - (5 years) - all main servers: 1436427
  • No. of tool users - (all time) - all main servers: 1446550
  • Tool usage (5 years) - - all main servers: 9024
  • Tool usage (all time) - all main - servers: 9272
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: Mass screening of contigs for antiobiotic resistance genes title_md: abricate - - description_md: '
  • Galaxy tool ids: abritamr
  • Description: - A pipeline for running AMRfinderPlus and collating results into functional classes
  • bio.tool - id: abritamr
  • bio.tool ids: abritamr
  • biii: - nan
  • bio.tool name: abriTAMR
  • 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.
  • EDAM operation: - Antimicrobial resistance prediction
  • EDAM topic: Microbiology, - Public health and epidemiology, Infectious disease
  • Status: - Up-to-date
  • Source: https://zenodo.org/record/7370628
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: abritamr
  • Date - of first commit of the suite: 2023-04-03
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr
  • Galaxy - wrapper version: 1.0.19
  • Conda id: abritamr
  • Conda - version: 1.0.19
  • EDAM operation (no superclasses): - Antimicrobial resistance prediction
  • EDAM topic (no superclasses): - Microbiology, Public health and epidemiology, Infectious disease
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1139
  • No. of tool - users (all time) (usegalaxy.eu): 1139
  • Tool usage (5 years) - (usegalaxy.eu): 109
  • Tool usage (all time) (usegalaxy.eu): - 109
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1139
  • No. - of tool users (all time) - all main servers: 1139
  • Tool - usage (5 years) - all main servers: 109
  • Tool usage (all - time) - all main servers: 109
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: A pipeline for running AMRfinderPlus and collating results into + functional classes title_md: abritamr - - description_md: '
  • Galaxy tool ids: abyss-pe
  • Description: - Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
  • bio.tool - id: abyss
  • bio.tool ids: abyss
  • biii: - nan
  • bio.tool name: ABySS
  • bio.tool description: - De novo genome sequence assembler using short reads.
  • EDAM operation: - Genome assembly, De-novo assembly, Scaffolding
  • EDAM topic: - Sequence assembly
  • Status: Up-to-date
  • Source: - http://www.bcgsc.ca/platform/bioinfo/software/abyss
  • ToolShed categories: - Assembly
  • ToolShed id: abyss
  • Date of first - commit of the suite: 2015-04-14
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss
  • Galaxy - wrapper version: 2.3.9
  • Conda id: abyss
  • Conda - version: 2.3.9
  • EDAM operation (no superclasses): - Genome assembly, De-novo assembly, Scaffolding
  • EDAM topic (no - superclasses): Sequence assembly
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 5543
  • No. of tool users (all time) (usegalaxy.eu): 5543
  • Tool - usage (5 years) (usegalaxy.eu): 1042
  • Tool usage (all time) - (usegalaxy.eu): 1042
  • No. of tool users (5 years) (usegalaxy.org): - 1301
  • No. of tool users (all time) (usegalaxy.org): 1305
  • Tool - usage (5 years) (usegalaxy.org): 413
  • Tool usage (all time) - (usegalaxy.org): 414
  • No. of tool users (5 years) (usegalaxy.org.au): - 2030
  • No. of tool users (all time) (usegalaxy.org.au): 2030
  • Tool - usage (5 years) (usegalaxy.org.au): 299
  • Tool usage (all - time) (usegalaxy.org.au): 299
  • No. of tool users (5 years) - - all main servers: 8874
  • No. of tool users (all time) - - all main servers: 8878
  • Tool usage (5 years) - all main - servers: 1754
  • Tool usage (all time) - all main servers: - 1755
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Assembly By Short Sequences - a de novo, parallel, paired-end + sequence assembler title_md: abyss - - description_md: '
  • Galaxy tool ids: aldex2
  • Description: - Performs analysis Of differential abundance taking sample variation into account
  • bio.tool - id: aldex2
  • bio.tool ids: aldex2
  • biii: - nan
  • bio.tool name: ALDEx2
  • 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.
  • EDAM - operation: Statistical inference
  • EDAM topic: Gene - expression, Statistics and probability
  • Status: To update
  • Source: - https://github.com/ggloor/ALDEx_bioc
  • ToolShed categories: - Metagenomics
  • ToolShed id: aldex2
  • Date of - first commit of the suite: 2022-06-29
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2
  • Galaxy - wrapper version: 1.26.0
  • Conda id: bioconductor-aldex2
  • Conda - version: 1.34.0
  • EDAM operation (no superclasses): - Statistical inference
  • EDAM topic (no superclasses): Gene - expression, Statistics and probability
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 262
  • No. of tool users (all time) (usegalaxy.eu): 262
  • Tool - usage (5 years) (usegalaxy.eu): 36
  • Tool usage (all time) - (usegalaxy.eu): 36
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 262
  • No. of tool users (all time) - all main - servers: 262
  • Tool usage (5 years) - all main servers: - 36
  • Tool usage (all time) - all main servers: 36
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Performs analysis Of differential abundance taking sample variation + into account title_md: aldex2 - - description_md: '
  • Galaxy tool ids: amplican
  • Description: - AmpliCan is an analysis tool for genome editing.
  • bio.tool id: - amplican
  • bio.tool ids: amplican
  • biii: - nan
  • bio.tool name: amplican
  • 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.
  • EDAM operation: Alignment, Standardisation - and normalisation
  • EDAM topic: PCR experiment, Statistics - and probability
  • Status: To update
  • Source: - https://github.com/valenlab/amplican
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: amplican
  • Date - of first commit of the suite: 2021-09-22
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican
  • Galaxy - wrapper version: 1.14.0
  • Conda id: bioconductor-amplican
  • Conda - version: 1.24.0
  • EDAM operation (no superclasses): - Alignment, Standardisation and normalisation
  • EDAM topic (no superclasses): - PCR experiment, Statistics and probability
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 81
  • No. of tool users (all time) (usegalaxy.eu): 81
  • Tool - usage (5 years) (usegalaxy.eu): 17
  • Tool usage (all time) - (usegalaxy.eu): 17
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 81
  • No. of tool users (all time) - all main - servers: 81
  • Tool usage (5 years) - all main servers: - 17
  • Tool usage (all time) - all main servers: 17
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: AmpliCan is an analysis tool for genome editing. title_md: amplican - - description_md: '
  • Galaxy tool ids: amrfinderplus
  • 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
  • biii: nan
  • bio.tool - name: AMRFinderPlus
  • 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
  • EDAM - operation: Antimicrobial resistance prediction
  • EDAM topic: - Microbiology, Public health and epidemiology, Infectious disease
  • Status: - Up-to-date
  • Source: https://github.com/ncbi/amr
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: AMRFinderPlus
  • Date - of first commit of the suite: 2023-05-12
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus
  • Galaxy - wrapper version: 3.12.8
  • Conda id: ncbi-amrfinderplus
  • Conda - version: 3.12.8
  • EDAM operation (no superclasses): - Antimicrobial resistance prediction
  • EDAM topic (no superclasses): - Microbiology, Public health and epidemiology, Infectious disease
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 5734
  • No. of tool - users (all time) (usegalaxy.eu): 5734
  • Tool usage (5 years) - (usegalaxy.eu): 334
  • Tool usage (all time) (usegalaxy.eu): - 334
  • No. of tool users (5 years) (usegalaxy.org): 1035
  • No. - of tool users (all time) (usegalaxy.org): 1035
  • Tool usage - (5 years) (usegalaxy.org): 106
  • Tool usage (all time) (usegalaxy.org): - 106
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 6769
  • No. - of tool users (all time) - all main servers: 6769
  • Tool - usage (5 years) - all main servers: 440
  • Tool usage (all - time) - all main servers: 440
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: '"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.' title_md: amrfinderplus - - description_md: '
  • Galaxy tool ids: ancombc
  • Description: - Performs analysis of compositions of microbiomes with bias correction.
  • bio.tool - id: ancombc
  • bio.tool ids: ancombc
  • biii: - nan
  • bio.tool name: ANCOMBC
  • 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.
  • EDAM operation: - DNA barcoding
  • EDAM topic: Microbial ecology, Metagenomics, - Taxonomy
  • Status: To update
  • Source: - https://github.com/FrederickHuangLin/ANCOMBC
  • ToolShed categories: - Metagenomics
  • ToolShed id: ancombc
  • Date of - first commit of the suite: 2022-07-16
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc
  • Galaxy - wrapper version: 1.4.0
  • Conda id: bioconductor-ancombc
  • Conda - version: 2.4.0
  • EDAM operation (no superclasses): - DNA barcoding
  • EDAM topic (no superclasses): Microbial ecology, - Metagenomics, Taxonomy
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 26
  • No. of tool users (all time) (usegalaxy.eu): 26
  • Tool - usage (5 years) (usegalaxy.eu): 7
  • Tool usage (all time) - (usegalaxy.eu): 7
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 26
  • No. of tool users (all time) - all main - servers: 26
  • Tool usage (5 years) - all main servers: - 7
  • Tool usage (all time) - all main servers: 7
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Performs analysis of compositions of microbiomes with bias correction. title_md: ancombc - - description_md: '
  • Galaxy tool ids: antismash
  • Description: - Antismash allows the genome-wide identification, annotation and analysis of - secondary metabolite biosynthesis gene clusters
  • bio.tool id: - antismash
  • bio.tool ids: antismash
  • biii: - nan
  • bio.tool name: antiSMASH
  • bio.tool description: - Rapid 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.
  • EDAM operation: Sequence - clustering, Gene prediction, Differential gene expression analysis
  • EDAM - topic: Molecular interactions, pathways and networks, Gene and protein - families
  • Status: To update
  • Source: - https://antismash.secondarymetabolites.org
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: antismash
  • Date - of first commit of the suite: 2015-02-28
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/antismash
  • Galaxy - wrapper version: 6.1.1
  • Conda id: antismash
  • Conda - version: 7.1.0
  • EDAM operation (no superclasses): - Sequence clustering, Gene prediction, Differential gene expression analysis
  • EDAM - topic (no superclasses): Molecular interactions, pathways and networks, - Gene and protein families
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 15949
  • No. of tool users (all time) (usegalaxy.eu): 16490
  • Tool - usage (5 years) (usegalaxy.eu): 726
  • Tool usage (all time) - (usegalaxy.eu): 811
  • No. of tool users (5 years) (usegalaxy.org): - 5113
  • No. of tool users (all time) (usegalaxy.org): 5113
  • Tool - usage (5 years) (usegalaxy.org): 649
  • Tool usage (all time) - (usegalaxy.org): 649
  • No. of tool users (5 years) (usegalaxy.org.au): - 6043
  • No. of tool users (all time) (usegalaxy.org.au): 6043
  • Tool - usage (5 years) (usegalaxy.org.au): 169
  • Tool usage (all - time) (usegalaxy.org.au): 169
  • No. of tool users (5 years) - - all main servers: 27105
  • No. of tool users (all time) - - all main servers: 27646
  • Tool usage (5 years) - all main - servers: 1544
  • Tool usage (all time) - all main servers: - 1629
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Antismash allows the genome-wide identification, annotation and + analysis of secondary metabolite biosynthesis gene clusters title_md: antismash - - description_md: '
  • Galaxy tool ids: artic_guppyplex, artic_minion
  • 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
  • bio.tool id: artic
  • bio.tool ids: - artic
  • biii: nan
  • bio.tool name: ARTIC
  • bio.tool - description: A bioinformatics pipeline for working with virus sequencing - data sequenced with nanopore
  • EDAM operation: Sequence alignment
  • EDAM - topic: Genomics
  • Status: To update
  • Source: - https://github.com/artic-network/fieldbioinformatics
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: nan
  • Date - of first commit of the suite: 2020-04-22
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic
  • Galaxy - wrapper version: nan
  • Conda id: artic
  • Conda - version: 1.2.4
  • EDAM operation (no superclasses): - Sequence alignment
  • EDAM topic (no superclasses): Genomics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 2
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 2
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 9021
  • No. of tool - users (all time) (usegalaxy.eu): 9021
  • Tool usage (5 years) - (usegalaxy.eu): 238
  • Tool usage (all time) (usegalaxy.eu): - 238
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 9021
  • No. - of tool users (all time) - all main servers: 9021
  • Tool - usage (5 years) - all main servers: 238
  • Tool usage (all - time) - all main servers: 238
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: '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' title_md: artic - - description_md: '
  • Galaxy tool ids: assemblystats
  • Description: - Summarise an assembly (e.g. N50 metrics)
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://github.com/phac-nml/galaxy_tools
  • ToolShed categories: - Assembly
  • ToolShed id: assemblystats
  • Date - of first commit of the suite: 2017-10-13
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats
  • Galaxy - wrapper version: 1.1.0
  • Conda id: perl-bioperl
  • Conda - version: 1.7.8
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Summarise an assembly (e.g. N50 metrics) title_md: assemblystats - - description_md: '
  • Galaxy tool ids: bakta
  • 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."
  • bio.tool id: bakta
  • bio.tool - ids: bakta
  • biii: nan
  • bio.tool name: - Bakta
  • bio.tool description: Rapid & standardized annotation - of bacterial genomes, MAGs & plasmids
  • EDAM operation: Genome - annotation
  • EDAM topic: Genomics, Data submission, annotation - and curation, Sequence analysis
  • Status: Up-to-date
  • Source: - https://github.com/oschwengers/bakta
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: bakta
  • Date - of first commit of the suite: 2022-09-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta
  • Galaxy - wrapper version: 1.9.4
  • Conda id: bakta
  • Conda - version: 1.9.4
  • EDAM operation (no superclasses): - Genome annotation
  • EDAM topic (no superclasses): Genomics, - Data submission, annotation and curation, Sequence analysis
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 11117
  • No. of tool - users (all time) (usegalaxy.eu): 11117
  • Tool usage (5 years) - (usegalaxy.eu): 534
  • Tool usage (all time) (usegalaxy.eu): - 534
  • No. of tool users (5 years) (usegalaxy.org): 19
  • No. - of tool users (all time) (usegalaxy.org): 19
  • Tool usage - (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): - 1
  • No. of tool users (5 years) (usegalaxy.org.au): 9601
  • No. - of tool users (all time) (usegalaxy.org.au): 9601
  • Tool - usage (5 years) (usegalaxy.org.au): 167
  • Tool usage (all - time) (usegalaxy.org.au): 167
  • No. of tool users (5 years) - - all main servers: 20737
  • No. of tool users (all time) - - all main servers: 20737
  • Tool usage (5 years) - all main - servers: 702
  • Tool usage (all time) - all main servers: - 702
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: '"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."' title_md: bakta - - description_md: '
  • Galaxy tool ids: bamtools
  • Description: - Operate on and transform BAM datasets in various ways using bamtools
  • bio.tool - id: bamtools
  • bio.tool ids: bamtools
  • biii: - nan
  • bio.tool name: BamTools
  • bio.tool description: - BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and - managing BAM files.
  • EDAM operation: Data handling, Sequence - alignment analysis
  • EDAM topic: Sequencing, Data management, - Sequence analysis
  • Status: Up-to-date
  • Source: - https://github.com/pezmaster31/bamtools
  • ToolShed categories: - Sequence Analysis, SAM
  • ToolShed id: bamtools
  • Date - of first commit of the suite: 2017-06-09
  • Galaxy wrapper - owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools
  • Galaxy - wrapper version: 2.5.2
  • Conda id: bamtools
  • Conda - version: 2.5.2
  • EDAM operation (no superclasses): - Data handling, Sequence alignment analysis
  • EDAM topic (no superclasses): - Sequencing, Sequence analysis
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 14693
  • No. of tool users (all time) (usegalaxy.eu): 15620
  • Tool - usage (5 years) (usegalaxy.eu): 653
  • Tool usage (all time) - (usegalaxy.eu): 721
  • No. of tool users (5 years) (usegalaxy.org): - 61872
  • No. of tool users (all time) (usegalaxy.org): 101400
  • Tool - usage (5 years) (usegalaxy.org): 1656
  • Tool usage (all time) - (usegalaxy.org): 5678
  • No. of tool users (5 years) (usegalaxy.org.au): - 39
  • No. of tool users (all time) (usegalaxy.org.au): 39
  • Tool - usage (5 years) (usegalaxy.org.au): 3
  • Tool usage (all time) - (usegalaxy.org.au): 3
  • No. of tool users (5 years) - all - main servers: 76604
  • No. of tool users (all time) - all - main servers: 117059
  • Tool usage (5 years) - all main servers: - 2312
  • Tool usage (all time) - all main servers: 6402
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Operate on and transform BAM datasets in various ways using bamtools title_md: bamtools - - description_md: '
  • Galaxy tool ids: bandage_image, bandage_info
  • Description: - Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs - Easily
  • bio.tool id: bandage
  • bio.tool ids: - bandage
  • biii: nan
  • bio.tool name: Bandage
  • 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.
  • EDAM - operation: Sequence assembly visualisation
  • EDAM topic: - Genomics, Sequence assembly
  • Status: Up-to-date
  • Source: - https://github.com/rrwick/Bandage
  • ToolShed categories: - Visualization
  • ToolShed id: bandage
  • Date of - first commit of the suite: 2018-09-14
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage
  • Galaxy - wrapper version: 2022.09
  • Conda id: bandage_ng
  • Conda - version: 2022.09
  • EDAM operation (no superclasses): - Sequence assembly visualisation
  • EDAM topic (no superclasses): - Genomics, Sequence assembly
  • Available on UseGalaxy.org (Main): - 2
  • Available on UseGalaxy.org.au: 2
  • Available - on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 2
  • Tools - available on UseGalaxy.org (Main): 2
  • Tools available on - UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu: - 2
  • Tools available on UseGalaxy.fr: 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: 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.no: 2
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 55392
  • No. of tool users (all time) (usegalaxy.eu): 56095
  • Tool - usage (5 years) (usegalaxy.eu): 4951
  • Tool usage (all time) - (usegalaxy.eu): 5035
  • No. of tool users (5 years) (usegalaxy.org): - 47603
  • No. of tool users (all time) (usegalaxy.org): 47603
  • Tool - usage (5 years) (usegalaxy.org): 4916
  • Tool usage (all time) - (usegalaxy.org): 4916
  • No. of tool users (5 years) (usegalaxy.org.au): - 18089
  • No. of tool users (all time) (usegalaxy.org.au): - 18089
  • Tool usage (5 years) (usegalaxy.org.au): 3121
  • Tool - usage (all time) (usegalaxy.org.au): 3121
  • No. of tool users - (5 years) - all main servers: 121084
  • No. of tool users - (all time) - all main servers: 121787
  • Tool usage (5 years) - - all main servers: 12988
  • Tool usage (all time) - all main - servers: 13072
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: Bandage - A Bioinformatics Application for Navigating De novo + Assembly Graphs Easily title_md: bandage - - description_md: '
  • Galaxy tool ids: BayeScan
  • Description: - Detecting natural selection from population-based genetic data
  • bio.tool - id: bayescan
  • bio.tool ids: bayescan
  • biii: - nan
  • bio.tool name: BayeScan
  • 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.
  • EDAM - operation: Statistical inference
  • EDAM topic: Genetics, - Evolutionary biology, Statistics and probability, DNA polymorphism
  • Status: - To update
  • Source: http://cmpg.unibe.ch/software/BayeScan/index.html
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: bayescan
  • Date - of first commit of the suite: 2017-03-09
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan
  • Galaxy - wrapper version: 2.1
  • Conda id: bayescan
  • Conda - version: 2.0.1
  • EDAM operation (no superclasses): - Statistical inference
  • EDAM topic (no superclasses): Genetics, - Evolutionary biology, Statistics and probability, DNA polymorphism
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 90
  • No. of tool - users (all time) (usegalaxy.eu): 90
  • Tool usage (5 years) - (usegalaxy.eu): 28
  • Tool usage (all time) (usegalaxy.eu): - 28
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 90
  • No. - of tool users (all time) - all main servers: 90
  • Tool usage - (5 years) - all main servers: 28
  • Tool usage (all time) - - all main servers: 28
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Detecting natural selection from population-based genetic data title_md: bayescan - - description_md: '
  • Galaxy tool ids: bbtools_bbduk, bbtools_bbmap, - bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole
  • 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.
  • bio.tool id: bbmap
  • bio.tool - ids: bbmap, bbtools
  • biii: nan
  • bio.tool - name: BBMap
  • 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.
  • EDAM operation: 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
  • Status: - To update
  • Source: https://jgi.doe.gov/data-and-tools/bbtools/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: bbtools
  • Date - of first commit of the suite: 2021-10-04
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools
  • Galaxy - wrapper version: 39.08
  • Conda id: bbmap
  • Conda - version: 39.10
  • EDAM operation (no superclasses): - RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, - Read binning, Sequence alignment
  • EDAM topic (no superclasses): - RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq
  • Available - on UseGalaxy.org (Main): 6
  • Available on UseGalaxy.org.au: - 3
  • Available on UseGalaxy.eu: 5
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 6
  • Tools available on UseGalaxy.org.au: 3
  • Tools - available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 11989
  • No. of tool - users (all time) (usegalaxy.eu): 11989
  • Tool usage (5 years) - (usegalaxy.eu): 768
  • Tool usage (all time) (usegalaxy.eu): - 768
  • No. of tool users (5 years) (usegalaxy.org): 4458
  • No. - of tool users (all time) (usegalaxy.org): 4458
  • Tool usage - (5 years) (usegalaxy.org): 652
  • Tool usage (all time) (usegalaxy.org): - 652
  • No. of tool users (5 years) (usegalaxy.org.au): 2507
  • No. - of tool users (all time) (usegalaxy.org.au): 2507
  • Tool - usage (5 years) (usegalaxy.org.au): 80
  • Tool usage (all - time) (usegalaxy.org.au): 80
  • No. of tool users (5 years) - - all main servers: 18954
  • No. of tool users (all time) - - all main servers: 18954
  • Tool usage (5 years) - all main - servers: 1500
  • Tool usage (all time) - all main servers: - 1500
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: 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. title_md: bbtools - - description_md: '
  • Galaxy tool ids: bigscape
  • Description: - Construct sequence similarity networks of BGCs and groups them into GCF
  • bio.tool - id: BiG-SCAPE
  • bio.tool ids: BiG-SCAPE
  • biii: - nan
  • bio.tool name: BiG-SCAPE
  • 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.
  • EDAM operation: Clustering, - Global alignment, Fold recognition
  • EDAM topic: Phylogeny, - Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families
  • Status: - Up-to-date
  • Source: https://github.com/medema-group/BiG-SCAPE
  • ToolShed - categories: Metagenomics
  • ToolShed id: bigscape
  • Date - of first commit of the suite: 2024-02-18
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape
  • Galaxy - wrapper version: 1.1.9
  • Conda id: bigscape
  • Conda - version: 1.1.9
  • EDAM operation (no superclasses): - Clustering, Global alignment, Fold recognition
  • EDAM topic (no - superclasses): Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, - Gene and protein families
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 544
  • No. of tool users (all time) (usegalaxy.eu): 544
  • Tool - usage (5 years) (usegalaxy.eu): 20
  • Tool usage (all time) - (usegalaxy.eu): 20
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 544
  • No. of tool users (all time) - all main - servers: 544
  • Tool usage (5 years) - all main servers: - 20
  • Tool usage (all time) - all main servers: 20
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Construct sequence similarity networks of BGCs and groups them + into GCF title_md: bigscape - - description_md: '
  • Galaxy tool ids: bin_refiner
  • Description: - Reconciles the outputs of different binning programs with the aim to improve - the quality of genome bins,especially with respect to contamination levels.
  • bio.tool - id: binning_refiner
  • bio.tool ids: binning_refiner
  • biii: - nan
  • bio.tool name: Binning_refiner
  • bio.tool - description: Improving genome bins through the combination of different - binning programs
  • EDAM operation: Read binning, Sequence - clustering
  • EDAM topic: Metagenomics, Sequence assembly, - Microbial ecology
  • Status: Up-to-date
  • Source: - https://github.com/songweizhi/Binning_refiner
  • ToolShed categories: - Metagenomics
  • ToolShed id: binning_refiner
  • Date - of first commit of the suite: 2022-02-18
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner
  • Galaxy - wrapper version: 1.4.3
  • Conda id: binning_refiner
  • Conda - version: 1.4.3
  • EDAM operation (no superclasses): - Read binning, Sequence clustering
  • EDAM topic (no superclasses): - Metagenomics, Sequence assembly, Microbial ecology
  • Available on - UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 126
  • No. of tool - users (all time) (usegalaxy.eu): 126
  • Tool usage (5 years) - (usegalaxy.eu): 42
  • Tool usage (all time) (usegalaxy.eu): - 42
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 126
  • No. - of tool users (all time) - all main servers: 126
  • Tool usage - (5 years) - all main servers: 42
  • Tool usage (all time) - - all main servers: 42
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Reconciles the outputs of different binning programs with the + aim to improve the quality of genome bins,especially with respect to contamination + levels. title_md: binning_refiner - - description_md: '
  • Galaxy tool ids: biohansel
  • Description: - Heidelberg and Enteritidis SNP Elucidation
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: https://github.com/phac-nml/biohansel
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: biohansel
  • Date - of first commit of the suite: 2018-08-01
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/biohansel
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel
  • Galaxy - wrapper version: 2.4.0
  • Conda id: bio_hansel
  • Conda - version: 2.6.1
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Heidelberg and Enteritidis SNP Elucidation title_md: biohansel - - description_md: '
  • Galaxy tool ids: biom_add_metadata, biom_convert, - biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table
  • Description: - The biom-format package provides a command line interface and Python API for - working with BIOM files.
  • bio.tool id: biomformat
  • bio.tool - ids: biomformat
  • biii: nan
  • bio.tool - name: biomformat
  • 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.
  • EDAM - operation: Formatting
  • EDAM topic: Laboratory information - management, Sequence analysis
  • Status: To update
  • Source: - https://github.com/biocore/biom-format
  • ToolShed categories: - Metagenomics
  • ToolShed id: nan
  • Date of first - commit of the suite: 2016-06-07
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format
  • Galaxy - wrapper version: 2.1.15
  • Conda id: biom-format
  • Conda - version: 2.1.7
  • EDAM operation (no superclasses): - Formatting
  • EDAM topic (no superclasses): Laboratory information - management, Sequence analysis
  • Available on UseGalaxy.org (Main): - 2
  • Available on UseGalaxy.org.au: 2
  • Available - on UseGalaxy.eu: 6
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 2
  • Tools available on - UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu: - 6
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 12725
  • No. of tool users (all time) (usegalaxy.eu): 12725
  • Tool - usage (5 years) (usegalaxy.eu): 297
  • Tool usage (all time) - (usegalaxy.eu): 297
  • No. of tool users (5 years) (usegalaxy.org): - 2851
  • No. of tool users (all time) (usegalaxy.org): 5049
  • Tool - usage (5 years) (usegalaxy.org): 450
  • Tool usage (all time) - (usegalaxy.org): 638
  • No. of tool users (5 years) (usegalaxy.org.au): - 2171
  • No. of tool users (all time) (usegalaxy.org.au): 2371
  • Tool - usage (5 years) (usegalaxy.org.au): 214
  • Tool usage (all - time) (usegalaxy.org.au): 239
  • No. of tool users (5 years) - - all main servers: 17747
  • No. of tool users (all time) - - all main servers: 20145
  • Tool usage (5 years) - all main - servers: 961
  • Tool usage (all time) - all main servers: - 1174
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: The biom-format package provides a command line interface and + Python API for working with BIOM files. title_md: biom_format - - description_md: '
  • Galaxy tool ids: bacteria_tradis, tradis_essentiality, - tradis_gene_insert_sites
  • Description: Bio-Tradis is a tool - suite dedicated to essentiality analyses with TraDis data.
  • bio.tool - id: biotradis
  • bio.tool ids: biotradis
  • biii: - nan
  • bio.tool name: biotradis
  • 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.
  • EDAM operation: Sequence analysis
  • EDAM - topic: Mobile genetic elements, Workflows
  • Status: - Up-to-date
  • Source: https://www.sanger.ac.uk/science/tools/bio-tradis
  • ToolShed - categories: Genome annotation
  • ToolShed id: biotradis
  • Date - of first commit of the suite: 2020-01-17
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis
  • Galaxy - wrapper version: 1.4.5
  • Conda id: biotradis
  • Conda - version: 1.4.5
  • EDAM operation (no superclasses): - Sequence analysis
  • EDAM topic (no superclasses): Mobile - genetic elements, Workflows
  • Available on UseGalaxy.org (Main): - 3
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 3
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 6243
  • No. of tool users (all time) (usegalaxy.org): 6243
  • Tool - usage (5 years) (usegalaxy.org): 375
  • Tool usage (all time) - (usegalaxy.org): 375
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 6243
  • No. of tool users (all time) - all main - servers: 6243
  • Tool usage (5 years) - all main servers: - 375
  • Tool usage (all time) - all main servers: 375
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Bio-Tradis is a tool suite dedicated to essentiality analyses + with TraDis data. title_md: biotradis - - description_md: '
  • Galaxy tool ids: blast2go
  • Description: - Maps BLAST results to GO annotation terms
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
  • ToolShed - categories: Ontology Manipulation, Sequence Analysis
  • ToolShed - id: blast2go
  • Date of first commit of the suite: - 2015-12-08
  • Galaxy wrapper owner: peterjc
  • Galaxy - wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
  • Galaxy - wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
  • Galaxy - wrapper version: 0.0.11
  • Conda id: b2g4pipe
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1063
  • No. of tool users (all time) (usegalaxy.eu): 1237
  • Tool - usage (5 years) (usegalaxy.eu): 257
  • Tool usage (all time) - (usegalaxy.eu): 300
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 1063
  • No. of tool users (all time) - all main - servers: 1237
  • Tool usage (5 years) - all main servers: - 257
  • Tool usage (all time) - all main servers: 300
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Maps BLAST results to GO annotation terms title_md: blast2go - - description_md: '
  • Galaxy tool ids: blast_reciprocal_best_hits
  • Description: - BLAST Reciprocal Best Hits (RBH) from two FASTA files
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
  • ToolShed - categories: Fasta Manipulation, Sequence Analysis
  • ToolShed - id: blast_rbh
  • Date of first commit of the suite: - 2016-12-05
  • Galaxy wrapper owner: peterjc
  • Galaxy - wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
  • Galaxy - wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
  • Galaxy - wrapper version: 0.3.0
  • Conda id: biopython
  • Conda - version: 1.70
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 24916
  • No. of tool - users (all time) (usegalaxy.eu): 27120
  • Tool usage (5 years) - (usegalaxy.eu): 283
  • Tool usage (all time) (usegalaxy.eu): - 347
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 24916
  • No. - of tool users (all time) - all main servers: 27120
  • Tool - usage (5 years) - all main servers: 283
  • Tool usage (all - time) - all main servers: 347
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: BLAST Reciprocal Best Hits (RBH) from two FASTA files title_md: blast_rbh - - description_md: '
  • Galaxy tool ids: blastxml_to_top_descr
  • Description: - Make table of top BLAST match descriptions
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
  • ToolShed - categories: Convert Formats, Sequence Analysis, Text Manipulation
  • ToolShed - id: blastxml_to_top_descr
  • Date of first commit of the suite: - 2015-05-21
  • Galaxy wrapper owner: peterjc
  • Galaxy - wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
  • Galaxy - wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
  • Galaxy - wrapper version: 0.1.2
  • Conda id: python
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 264392
  • No. of tool users (all time) (usegalaxy.eu): 265217
  • Tool - usage (5 years) (usegalaxy.eu): 483
  • Tool usage (all time) - (usegalaxy.eu): 552
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 264392
  • No. of tool users (all time) - all - main servers: 265217
  • Tool usage (5 years) - all main servers: - 483
  • Tool usage (all time) - all main servers: 552
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Make table of top BLAST match descriptions title_md: blastxml_to_top_descr - - description_md: '
  • Galaxy tool ids: est_abundance
  • Description: - Bayesian Reestimation of Abundance with KrakEN
  • bio.tool id: - bracken
  • bio.tool ids: bracken
  • biii: - nan
  • bio.tool name: Bracken
  • bio.tool description: - Statistical method that computes the abundance of species in DNA sequences from - a metagenomics sample.
  • EDAM operation: Statistical calculation
  • EDAM - topic: Metagenomics, Microbial ecology
  • Status: Up-to-date
  • Source: - https://ccb.jhu.edu/software/bracken/
  • ToolShed categories: - Sequence Analysis, Metagenomics
  • ToolShed id: bracken
  • Date - of first commit of the suite: 2019-10-15
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken
  • Galaxy - wrapper version: 3.0
  • Conda id: bracken
  • Conda - version: 3.0
  • EDAM operation (no superclasses): Statistical - calculation
  • EDAM topic (no superclasses): Metagenomics, - Microbial ecology
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 51378
  • No. of tool - users (all time) (usegalaxy.eu): 51378
  • Tool usage (5 years) - (usegalaxy.eu): 775
  • Tool usage (all time) (usegalaxy.eu): - 775
  • No. of tool users (5 years) (usegalaxy.org): 3298
  • No. - of tool users (all time) (usegalaxy.org): 3298
  • Tool usage - (5 years) (usegalaxy.org): 160
  • Tool usage (all time) (usegalaxy.org): - 160
  • No. of tool users (5 years) (usegalaxy.org.au): 1660
  • No. - of tool users (all time) (usegalaxy.org.au): 1660
  • Tool - usage (5 years) (usegalaxy.org.au): 63
  • Tool usage (all - time) (usegalaxy.org.au): 63
  • No. of tool users (5 years) - - all main servers: 56336
  • No. of tool users (all time) - - all main servers: 56336
  • Tool usage (5 years) - all main - servers: 998
  • Tool usage (all time) - all main servers: - 998
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Bayesian Reestimation of Abundance with KrakEN title_md: bracken - - description_md: '
  • Galaxy tool ids: busco
  • Description: - BUSCO assess genome and annotation completeness
  • bio.tool id: - busco
  • bio.tool ids: busco
  • biii: nan
  • bio.tool - name: BUSCO
  • 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.
  • EDAM operation: Sequence - assembly validation, Scaffolding, Genome assembly, Transcriptome assembly
  • EDAM - topic: Sequence assembly, Genomics, Transcriptomics, Sequence analysis
  • Status: - To update
  • Source: https://gitlab.com/ezlab/busco/-/releases
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: busco
  • Date - of first commit of the suite: 2019-12-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco
  • Galaxy - wrapper version: 5.7.1
  • Conda id: busco
  • Conda - version: 5.8.0
  • EDAM operation (no superclasses): - Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly
  • EDAM - topic (no superclasses): Sequence assembly, Transcriptomics, Sequence - analysis
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 102717
  • No. of tool - users (all time) (usegalaxy.eu): 103051
  • Tool usage (5 years) - (usegalaxy.eu): 3877
  • Tool usage (all time) (usegalaxy.eu): - 3926
  • No. of tool users (5 years) (usegalaxy.org): 34251
  • No. - of tool users (all time) (usegalaxy.org): 34251
  • Tool usage - (5 years) (usegalaxy.org): 3506
  • Tool usage (all time) (usegalaxy.org): - 3506
  • No. of tool users (5 years) (usegalaxy.org.au): 33192
  • No. - of tool users (all time) (usegalaxy.org.au): 34369
  • Tool - usage (5 years) (usegalaxy.org.au): 2439
  • Tool usage (all - time) (usegalaxy.org.au): 2525
  • No. of tool users (5 years) - - all main servers: 170160
  • No. of tool users (all time) - - all main servers: 171671
  • Tool usage (5 years) - all main - servers: 9822
  • Tool usage (all time) - all main servers: - 9957
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: BUSCO assess genome and annotation completeness title_md: busco - - description_md: '
  • Galaxy tool ids: cat_add_names, cat_bins, - cat_contigs, cat_prepare, cat_summarise
  • Description: Contig - Annotation Tool (CAT)
  • bio.tool id: cat_bins
  • bio.tool - ids: cat_bins
  • biii: nan
  • bio.tool name: - CAT and BAT
  • 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.
  • EDAM - operation: Taxonomic classification, Sequence assembly, Coding region - prediction
  • EDAM topic: Metagenomics, Metagenomic sequencing, - Taxonomy, Sequence assembly
  • Status: To update
  • Source: - https://github.com/dutilh/CAT
  • ToolShed categories: Metagenomics
  • ToolShed - id: contig_annotation_tool
  • Date of first commit of the - suite: 2019-11-27
  • Galaxy wrapper owner: iuc
  • Galaxy - wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat
  • Galaxy - wrapper version: 5.2.3
  • Conda id: cat
  • Conda - version: 5.3
  • EDAM operation (no superclasses): Taxonomic - classification, Sequence assembly, Coding region prediction
  • EDAM - topic (no superclasses): Metagenomics, Metagenomic sequencing, Taxonomy, - Sequence assembly
  • Available on UseGalaxy.org (Main): 5
  • Available - on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: - 5
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 5
  • Tools available on UseGalaxy.org.au: - 2
  • Tools available on UseGalaxy.eu: 5
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 5
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 3835
  • No. of tool - users (all time) (usegalaxy.eu): 3835
  • Tool usage (5 years) - (usegalaxy.eu): 597
  • Tool usage (all time) (usegalaxy.eu): - 597
  • No. of tool users (5 years) (usegalaxy.org): 1359
  • No. - of tool users (all time) (usegalaxy.org): 1359
  • Tool usage - (5 years) (usegalaxy.org): 467
  • Tool usage (all time) (usegalaxy.org): - 467
  • No. of tool users (5 years) (usegalaxy.org.au): 646
  • No. - of tool users (all time) (usegalaxy.org.au): 646
  • Tool usage - (5 years) (usegalaxy.org.au): 98
  • Tool usage (all time) - (usegalaxy.org.au): 98
  • No. of tool users (5 years) - all - main servers: 5840
  • No. of tool users (all time) - all main - servers: 5840
  • Tool usage (5 years) - all main servers: - 1162
  • Tool usage (all time) - all main servers: 1162
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Contig Annotation Tool (CAT) title_md: cat - - description_md: '
  • Galaxy tool ids: cd_hit_dup
  • Description: - simple tool for removing duplicates from sequencing reads
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: nan
  • ToolShed - categories: Metagenomics, Sequence Analysis
  • ToolShed id: - cd_hit_dup
  • Date of first commit of the suite: 2015-04-28
  • Galaxy - wrapper owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup
  • Galaxy - wrapper version: 0.0.1
  • Conda id: cd-hit-auxtools
  • Conda - version: 4.8.1
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 5946
  • No. of tool - users (all time) (usegalaxy.org): 7379
  • Tool usage (5 years) - (usegalaxy.org): 407
  • Tool usage (all time) (usegalaxy.org): - 628
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 5946
  • No. - of tool users (all time) - all main servers: 7379
  • Tool - usage (5 years) - all main servers: 407
  • Tool usage (all - time) - all main servers: 628
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: simple tool for removing duplicates from sequencing reads title_md: cd_hit_dup - - description_md: '
  • Galaxy tool ids: cd_hit
  • Description: - Cluster or compare biological sequence datasets
  • bio.tool id: - cd-hit
  • bio.tool ids: cd-hit
  • biii: - nan
  • bio.tool name: cd-hit
  • bio.tool description: - Cluster a nucleotide dataset into representative sequences.
  • EDAM - operation: Sequence clustering
  • EDAM topic: Sequencing
  • Status: - Up-to-date
  • Source: http://weizhongli-lab.org/cd-hit/
  • ToolShed - categories: Sequence Analysis, Fasta Manipulation
  • ToolShed - id: cd_hit
  • Date of first commit of the suite: 2018-02-26
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit
  • Galaxy - wrapper version: 4.8.1
  • Conda id: cd-hit
  • Conda - version: 4.8.1
  • EDAM operation (no superclasses): - Sequence clustering
  • EDAM topic (no superclasses): Sequencing
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 10414
  • No. of tool - users (all time) (usegalaxy.eu): 10414
  • Tool usage (5 years) - (usegalaxy.eu): 510
  • Tool usage (all time) (usegalaxy.eu): - 510
  • No. of tool users (5 years) (usegalaxy.org): 2
  • No. - of tool users (all time) (usegalaxy.org): 2
  • Tool usage - (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): - 1
  • No. of tool users (5 years) (usegalaxy.org.au): 2
  • No. - of tool users (all time) (usegalaxy.org.au): 2
  • Tool usage - (5 years) (usegalaxy.org.au): 1
  • Tool usage (all time) (usegalaxy.org.au): - 1
  • No. of tool users (5 years) - all main servers: 10418
  • No. - of tool users (all time) - all main servers: 10418
  • Tool - usage (5 years) - all main servers: 512
  • Tool usage (all - time) - all main servers: 512
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Cluster or compare biological sequence datasets title_md: cdhit - - description_md: '
  • Galaxy tool ids: cemitool
  • Description: - Gene co-expression network analysis tool
  • bio.tool id: cemitool
  • bio.tool - ids: cemitool
  • biii: nan
  • bio.tool name: - CEMiTool
  • 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.
  • EDAM operation: Enrichment analysis, - Pathway or network analysis
  • EDAM topic: Gene expression, - Transcriptomics, Microarray experiment
  • Status: Up-to-date
  • Source: - https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html
  • ToolShed - categories: Transcriptomics, RNA, Statistics
  • ToolShed id: - cemitool
  • Date of first commit of the suite: 2022-10-10
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool
  • Galaxy - wrapper version: 1.26.0
  • Conda id: bioconductor-cemitool
  • Conda - version: 1.26.0
  • EDAM operation (no superclasses): - Enrichment analysis, Pathway or network analysis
  • EDAM topic (no - superclasses): Transcriptomics, Microarray experiment
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 225
  • No. of tool - users (all time) (usegalaxy.eu): 225
  • Tool usage (5 years) - (usegalaxy.eu): 32
  • Tool usage (all time) (usegalaxy.eu): - 32
  • No. of tool users (5 years) (usegalaxy.org): 271
  • No. - of tool users (all time) (usegalaxy.org): 271
  • Tool usage - (5 years) (usegalaxy.org): 61
  • Tool usage (all time) (usegalaxy.org): - 61
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 496
  • No. - of tool users (all time) - all main servers: 496
  • Tool usage - (5 years) - all main servers: 93
  • Tool usage (all time) - - all main servers: 93
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Gene co-expression network analysis tool title_md: cemitool - - description_md: '
  • 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
  • Description: - Assess the quality of microbial genomes recovered from isolates, single cells, - and metagenomes
  • bio.tool id: checkm
  • bio.tool - ids: checkm
  • biii: nan
  • bio.tool name: - CheckM
  • bio.tool description: CheckM provides a set of tools - for assessing the quality of genomes recovered from isolates, single cells, - or metagenomes.
  • EDAM operation: Sequence assembly validation, - Validation, Sequence composition calculation, Sequencing quality control, Statistical - calculation
  • EDAM topic: Genomics, Phylogenomics, Phylogenetics, - Taxonomy, Metagenomics, Data quality management
  • Status: - Up-to-date
  • Source: https://github.com/Ecogenomics/CheckM
  • ToolShed - categories: Metagenomics
  • ToolShed id: checkm
  • Date - of first commit of the suite: 2022-07-29
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm
  • Galaxy - wrapper version: 1.2.3
  • Conda id: checkm-genome
  • Conda - version: 1.2.3
  • EDAM operation (no superclasses): - Sequence assembly validation, Sequence composition calculation, Statistical - calculation
  • EDAM topic (no superclasses): Phylogenomics, - Phylogenetics, Taxonomy, Metagenomics, Data quality management
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 10
  • Available on UseGalaxy.eu: 10
  • Available - on UseGalaxy.fr: 10
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 10
  • Tools - available on UseGalaxy.eu: 10
  • Tools available on UseGalaxy.fr: - 10
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 7500
  • No. of tool - users (all time) (usegalaxy.eu): 7500
  • Tool usage (5 years) - (usegalaxy.eu): 930
  • Tool usage (all time) (usegalaxy.eu): - 930
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 7500
  • No. - of tool users (all time) - all main servers: 7500
  • Tool - usage (5 years) - all main servers: 930
  • Tool usage (all - time) - all main servers: 930
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Assess the quality of microbial genomes recovered from isolates, + single cells, and metagenomes title_md: checkm - - description_md: '
  • Galaxy tool ids: clair3
  • Description: - Symphonizing pileup and full-alignment for high-performance long-read variant - calling
  • bio.tool id: clair3
  • bio.tool ids: - clair3
  • biii: nan
  • bio.tool name: Clair3
  • 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.
  • EDAM operation: Variant calling
  • EDAM - topic: Molecular genetics
  • Status: To update
  • Source: - https://github.com/HKU-BAL/Clair3
  • ToolShed categories: - Sequence Analysis, Variant Analysis
  • ToolShed id: clair3
  • Date - of first commit of the suite: 2022-06-15
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3
  • Galaxy - wrapper version: 1.0.8
  • Conda id: clair3
  • Conda - version: 1.0.10
  • EDAM operation (no superclasses): - Variant calling
  • EDAM topic (no superclasses): Molecular - genetics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 3388
  • No. of tool - users (all time) (usegalaxy.eu): 3388
  • Tool usage (5 years) - (usegalaxy.eu): 187
  • Tool usage (all time) (usegalaxy.eu): - 187
  • No. of tool users (5 years) (usegalaxy.org): 1
  • No. - of tool users (all time) (usegalaxy.org): 1
  • Tool usage - (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): - 1
  • No. of tool users (5 years) (usegalaxy.org.au): 1
  • No. - of tool users (all time) (usegalaxy.org.au): 1
  • Tool usage - (5 years) (usegalaxy.org.au): 1
  • Tool usage (all time) (usegalaxy.org.au): - 1
  • No. of tool users (5 years) - all main servers: 3390
  • No. - of tool users (all time) - all main servers: 3390
  • Tool - usage (5 years) - all main servers: 189
  • Tool usage (all - time) - all main servers: 189
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Symphonizing pileup and full-alignment for high-performance long-read + variant calling title_md: clair3 - - description_md: '
  • Galaxy tool ids: clinod
  • Description: - NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins
  • bio.tool - id: clinod
  • bio.tool ids: clinod
  • biii: - nan
  • bio.tool name: clinod
  • 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.
  • EDAM - operation: Nucleic acid sequence analysis
  • EDAM topic: - Sequence analysis
  • Status: To update
  • Source: - http://www.compbio.dundee.ac.uk/www-nod/
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: clinod
  • Date - of first commit of the suite: 2014-02-18
  • Galaxy wrapper - owner: peterjc
  • Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
  • Galaxy - wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
  • Galaxy - wrapper version: 0.1.0
  • Conda id: clinod
  • Conda - version: 1.3
  • EDAM operation (no superclasses): Nucleic - acid sequence analysis
  • EDAM topic (no superclasses): Sequence - analysis
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 0
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 0
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 548
  • No. of tool - users (all time) (usegalaxy.org): 548
  • Tool usage (5 years) - (usegalaxy.org): 18
  • Tool usage (all time) (usegalaxy.org): - 18
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 548
  • No. - of tool users (all time) - all main servers: 548
  • Tool usage - (5 years) - all main servers: 18
  • Tool usage (all time) - - all main servers: 18
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: 'NoD: a Nucleolar localization sequence detector for eukaryotic + and viral proteins' title_md: clinod - - description_md: '
  • Galaxy tool ids: clustalw
  • Description: - ClustalW multiple sequence alignment program for DNA or proteins
  • bio.tool - id: clustal2
  • bio.tool ids: clustal2
  • biii: - nan
  • bio.tool name: Clustal 2 (Clustal W, Clustal X)
  • 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.
  • EDAM operation: Multiple - sequence alignment
  • EDAM topic: Phylogeny, Sequence analysis
  • Status: - Up-to-date
  • Source: http://www.clustal.org/clustal2/
  • ToolShed - categories: Phylogenetics, Sequence Analysis
  • ToolShed id: - clustalw
  • Date of first commit of the suite: 2022-10-02
  • Galaxy - wrapper owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw
  • Galaxy - wrapper version: 2.1
  • Conda id: clustalw
  • Conda - version: 2.1
  • EDAM operation (no superclasses): Multiple - sequence alignment
  • EDAM topic (no superclasses): Phylogeny, - Sequence analysis
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 79867
  • No. of tool - users (all time) (usegalaxy.eu): 80817
  • Tool usage (5 years) - (usegalaxy.eu): 1675
  • Tool usage (all time) (usegalaxy.eu): - 1785
  • No. of tool users (5 years) (usegalaxy.org): 49493
  • No. - of tool users (all time) (usegalaxy.org): 87884
  • Tool usage - (5 years) (usegalaxy.org): 3703
  • Tool usage (all time) (usegalaxy.org): - 7380
  • No. of tool users (5 years) (usegalaxy.org.au): 8797
  • No. - of tool users (all time) (usegalaxy.org.au): 9713
  • Tool - usage (5 years) (usegalaxy.org.au): 670
  • Tool usage (all - time) (usegalaxy.org.au): 728
  • No. of tool users (5 years) - - all main servers: 138157
  • No. of tool users (all time) - - all main servers: 178414
  • Tool usage (5 years) - all main - servers: 6048
  • Tool usage (all time) - all main servers: - 9893
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: ClustalW multiple sequence alignment program for DNA or proteins title_md: clustalw - - description_md: '
  • Galaxy tool ids: cmsearch_deoverlap
  • Description: - removes lower scoring overlaps from cmsearch results.
  • bio.tool - id: cmsearch-deoverlap
  • bio.tool ids: cmsearch-deoverlap
  • biii: - nan
  • bio.tool name: cmsearch-deoverlap
  • bio.tool - description: Removes lower scoring overlaps from cmsearch results.
  • EDAM - operation: Comparison, Alignment
  • EDAM topic: Biology, - Medicine
  • Status: To update
  • Source: - https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl
  • ToolShed - categories: RNA
  • ToolShed id: cmsearch_deoverlap
  • Date - of first commit of the suite: 2023-08-19
  • Galaxy wrapper - owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap
  • Galaxy - wrapper version: 0.08+galaxy2
  • Conda id: perl
  • Conda - version: nan
  • EDAM operation (no superclasses): Comparison, - Alignment
  • EDAM topic (no superclasses): Biology, Medicine
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 2609
  • No. of tool - users (all time) (usegalaxy.eu): 2609
  • Tool usage (5 years) - (usegalaxy.eu): 3
  • Tool usage (all time) (usegalaxy.eu): - 3
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 2609
  • No. - of tool users (all time) - all main servers: 2609
  • Tool - usage (5 years) - all main servers: 3
  • Tool usage (all time) - - all main servers: 3
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: removes lower scoring overlaps from cmsearch results. title_md: cmsearch_deoverlap - - description_md: '
  • Galaxy tool ids: codeml
  • Description: - Detects positive selection
  • bio.tool id: paml
  • bio.tool - ids: paml
  • biii: nan
  • bio.tool name: - PAML
  • bio.tool description: Package of programs for phylogenetic - analyses of DNA or protein sequences using maximum likelihood.
  • EDAM - operation: Probabilistic sequence generation, Phylogenetic tree generation - (maximum likelihood and Bayesian methods), Phylogenetic tree analysis
  • EDAM - topic: Phylogenetics, Sequence analysis
  • Status: - To update
  • Source: http://abacus.gene.ucl.ac.uk/software/paml.html
  • ToolShed - categories: Phylogenetics
  • ToolShed id: codeml
  • Date - of first commit of the suite: 2017-07-19
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml
  • Galaxy - wrapper version: 4.9
  • Conda id: paml
  • Conda - version: 4.10.7
  • EDAM operation (no superclasses): - Probabilistic sequence generation
  • EDAM topic (no superclasses): - Phylogenetics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 61197
  • No. of tool - users (all time) (usegalaxy.eu): 61220
  • Tool usage (5 years) - (usegalaxy.eu): 64
  • Tool usage (all time) (usegalaxy.eu): - 65
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 61197
  • No. - of tool users (all time) - all main servers: 61220
  • Tool - usage (5 years) - all main servers: 64
  • Tool usage (all - time) - all main servers: 65
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Detects positive selection title_md: codeml - - description_md: '
  • Galaxy tool ids: cooc_mutbamscan, cooc_pubmut, - cooc_tabmut
  • Description: co-occurrence of mutations on - amplicons
  • bio.tool id: cojac
  • bio.tool ids: - cojac
  • biii: nan
  • bio.tool name: COJAC
  • 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.
  • EDAM operation: - nan
  • EDAM topic: Genetic variation
  • Status: - Up-to-date
  • Source: https://github.com/cbg-ethz/cojac
  • ToolShed - categories: Metagenomics, Sequence Analysis
  • ToolShed id: - cojac
  • Date of first commit of the suite: 2022-08-11
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac
  • Galaxy - wrapper version: 0.9.2
  • Conda id: cojac
  • Conda - version: 0.9.2
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): Genetic variation
  • Available - on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 3
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 2
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 2758
  • No. of tool - users (all time) (usegalaxy.eu): 2758
  • Tool usage (5 years) - (usegalaxy.eu): 22
  • Tool usage (all time) (usegalaxy.eu): - 22
  • No. of tool users (5 years) (usegalaxy.org): 20
  • No. - of tool users (all time) (usegalaxy.org): 20
  • Tool usage - (5 years) (usegalaxy.org): 10
  • Tool usage (all time) (usegalaxy.org): - 10
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 2778
  • No. - of tool users (all time) - all main servers: 2778
  • Tool - usage (5 years) - all main servers: 32
  • Tool usage (all - time) - all main servers: 32
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: co-occurrence of mutations on amplicons title_md: cojac - - description_md: '
  • Galaxy tool ids: combine_stats
  • Description: - Combine multiple Assemblystats datasets into a single tabular report
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: https://github.com/phac-nml/galaxy_tools
  • ToolShed - categories: Assembly
  • ToolShed id: combine_assemblystats
  • Date - of first commit of the suite: 2017-11-08
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats
  • Galaxy - wrapper version: 1.0
  • Conda id: perl-getopt-long
  • Conda - version: 2.58
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Combine multiple Assemblystats datasets into a single tabular + report title_md: combine_assembly_stats - - description_md: '
  • Galaxy tool ids: combine_metaphlan_humann
  • Description: - Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and - gene families/pathways abundances
  • bio.tool id: combine_metaphlan_and_humann
  • bio.tool - ids: combine_metaphlan_and_humann
  • biii: nan
  • bio.tool - name: Combine Metaphlan and HUMAnN
  • bio.tool description: - This tool combine MetaPhlAn outputs and HUMANnN outputs
  • EDAM operation: - Aggregation
  • EDAM topic: Metagenomics, Molecular interactions, - pathways and networks
  • Status: To update
  • Source: - nan
  • ToolShed categories: Metagenomics
  • ToolShed - id: combine_metaphlan2_humann2
  • Date of first commit of - the suite: 2023-07-20
  • Galaxy wrapper owner: bebatut
  • Galaxy - wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann
  • Galaxy - wrapper version: 0.3.0
  • Conda id: python
  • Conda - version: nan
  • EDAM operation (no superclasses): Aggregation
  • EDAM - topic (no superclasses): Metagenomics, Molecular interactions, pathways - and networks
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 530
  • No. of tool - users (all time) (usegalaxy.eu): 530
  • Tool usage (5 years) - (usegalaxy.eu): 65
  • Tool usage (all time) (usegalaxy.eu): - 65
  • No. of tool users (5 years) (usegalaxy.org): 8
  • No. - of tool users (all time) (usegalaxy.org): 8
  • Tool usage - (5 years) (usegalaxy.org): 6
  • Tool usage (all time) (usegalaxy.org): - 6
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 538
  • No. - of tool users (all time) - all main servers: 538
  • Tool usage - (5 years) - all main servers: 71
  • Tool usage (all time) - - all main servers: 71
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species + abundances and gene families/pathways abundances title_md: combine_metaphlan_humann - - description_md: '
  • Galaxy tool ids: compare_humann2_output
  • Description: - Compare outputs of HUMAnN2 for several samples and extract similar and specific - information
  • bio.tool id: compare_humann2_outputs
  • bio.tool - ids: compare_humann2_outputs
  • biii: nan
  • bio.tool - name: Compare HUMAnN2 outputs
  • bio.tool description: - This tool compare HUMANnN2 outputs with gene families or pathways and their - relative abundances between several samples
  • EDAM operation: - Comparison
  • EDAM topic: Metagenomics, Gene and protein families
  • Status: - To update
  • Source: nan
  • ToolShed categories: - Metagenomics
  • ToolShed id: compare_humann2_output
  • Date - of first commit of the suite: 2022-10-19
  • Galaxy wrapper - owner: bebatut
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
  • Galaxy - wrapper version: 0.2.0
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): Comparison
  • EDAM - topic (no superclasses): Metagenomics, Gene and protein families
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 306
  • No. of tool - users (all time) (usegalaxy.eu): 332
  • Tool usage (5 years) - (usegalaxy.eu): 28
  • Tool usage (all time) (usegalaxy.eu): - 32
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 306
  • No. - of tool users (all time) - all main servers: 332
  • Tool usage - (5 years) - all main servers: 28
  • Tool usage (all time) - - all main servers: 32
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Compare outputs of HUMAnN2 for several samples and extract similar + and specific information title_md: compare_humann2_output - - description_md: '
  • Galaxy tool ids: compleasm
  • Description: - Compleasm: a faster and more accurate reimplementation of BUSCO
  • bio.tool - id: compleasm
  • bio.tool ids: compleasm
  • biii: - nan
  • bio.tool name: compleasm
  • bio.tool description: - "Compleasm: a faster and more accurate reimplementation of BUSCO"
  • EDAM - operation: Sequence assembly validation, Sequence analysis, Scaffolding, - Transcriptome assembly
  • EDAM topic: Sequence assembly, Genomics, - Transcriptomics, Sequence analysis
  • Status: Up-to-date
  • Source: - https://github.com/huangnengCSU/compleasm
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: compleasm
  • Date - of first commit of the suite: 2023-12-04
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm
  • Galaxy - wrapper version: 0.2.6
  • Conda id: compleasm
  • Conda - version: 0.2.6
  • EDAM operation (no superclasses): - Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome - assembly
  • EDAM topic (no superclasses): Sequence assembly, - Transcriptomics, Sequence analysis
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 266
  • No. of tool users (all time) (usegalaxy.eu): 266
  • Tool - usage (5 years) (usegalaxy.eu): 39
  • Tool usage (all time) - (usegalaxy.eu): 39
  • No. of tool users (5 years) (usegalaxy.org): - 28
  • No. of tool users (all time) (usegalaxy.org): 28
  • Tool - usage (5 years) (usegalaxy.org): 15
  • Tool usage (all time) - (usegalaxy.org): 15
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 294
  • No. of tool users (all time) - all main - servers: 294
  • Tool usage (5 years) - all main servers: - 54
  • Tool usage (all time) - all main servers: 54
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: 'Compleasm: a faster and more accurate reimplementation of BUSCO' title_md: compleasm - - description_md: '
  • Galaxy tool ids: concoct, concoct_coverage_table, - concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering
  • 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.
  • bio.tool id: concoct
  • bio.tool - ids: concoct
  • biii: nan
  • bio.tool name: - CONCOCT
  • 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.
  • EDAM - operation: Sequence clustering, Read binning
  • EDAM topic: - Metagenomics
  • Status: Up-to-date
  • Source: - https://github.com/BinPro/CONCOCT
  • ToolShed categories: - Metagenomics
  • ToolShed id: concoct
  • Date of - first commit of the suite: 2022-02-18
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct
  • Galaxy - wrapper version: 1.1.0
  • Conda id: concoct
  • Conda - version: 1.1.0
  • EDAM operation (no superclasses): - Sequence clustering, Read binning
  • EDAM topic (no superclasses): - Metagenomics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 5
  • Available on UseGalaxy.fr: 5
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 5
  • Tools - available on UseGalaxy.fr: 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 2105
  • No. of tool - users (all time) (usegalaxy.eu): 2105
  • Tool usage (5 years) - (usegalaxy.eu): 155
  • Tool usage (all time) (usegalaxy.eu): - 155
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 2105
  • No. - of tool users (all time) - all main servers: 2105
  • Tool - usage (5 years) - all main servers: 155
  • Tool usage (all - time) - all main servers: 155
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: 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. title_md: concoct - - description_md: '
  • Galaxy tool ids: coverm_contig, coverm_genome
  • Description: - CoverM genome and contig wrappers
  • bio.tool id: coverm
  • bio.tool - ids: coverm
  • biii: nan
  • bio.tool name: - CoverM
  • bio.tool description: Read coverage calculator for - metagenomics
  • EDAM operation: Local alignment
  • EDAM - topic: Bioinformatics
  • Status: Up-to-date
  • Source: - https://github.com/wwood/CoverM
  • ToolShed categories: Sequence - Analysis
  • ToolShed id: coverm
  • Date of first - commit of the suite: 2022-04-26
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tools/coverm
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm
  • Galaxy - wrapper version: 0.7.0
  • Conda id: coverm
  • Conda - version: 0.7.0
  • EDAM operation (no superclasses): - Local alignment
  • EDAM topic (no superclasses): Bioinformatics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: - 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1081
  • No. of tool - users (all time) (usegalaxy.eu): 1081
  • Tool usage (5 years) - (usegalaxy.eu): 151
  • Tool usage (all time) (usegalaxy.eu): - 151
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1081
  • No. - of tool users (all time) - all main servers: 1081
  • Tool - usage (5 years) - all main servers: 151
  • Tool usage (all - time) - all main servers: 151
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: CoverM genome and contig wrappers title_md: coverm - - description_md: '
  • Galaxy tool ids: CryptoGenotyper
  • Description: - CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype - based on SSU rRNA and gp60 markers.
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: - https://github.com/phac-nml/CryptoGenotyper
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: cryptogenotyper
  • Date - of first commit of the suite: 2020-10-14
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/CryptoGenotyper
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper
  • Galaxy - wrapper version: 1.0
  • Conda id: cryptogenotyper
  • Conda - version: 1.0
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 9942
  • No. of tool users (all time) (usegalaxy.eu): 9942
  • Tool - usage (5 years) (usegalaxy.eu): 26
  • Tool usage (all time) - (usegalaxy.eu): 26
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 9942
  • No. of tool users (all time) - all main - servers: 9942
  • Tool usage (5 years) - all main servers: - 26
  • Tool usage (all time) - all main servers: 26
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: CryptoGenotyper is a standalone tool to *in-silico* determine + species and subtype based on SSU rRNA and gp60 markers. title_md: cryptogenotyper - - description_md: '
  • Galaxy tool ids: cutadapt
  • Description: - Flexible tool to remove adapter sequences (and quality trim) high throughput - sequencing reads (fasta/fastq).
  • bio.tool id: cutadapt
  • bio.tool - ids: cutadapt
  • biii: nan
  • bio.tool name: - Cutadapt
  • bio.tool description: Find and remove adapter - sequences, primers, poly-A tails and other types of unwanted sequence from your - high-throughput sequencing reads.
  • EDAM operation: Sequence - trimming, Primer removal, Read pre-processing
  • EDAM topic: - Genomics, Probes and primers, Sequencing
  • Status: Up-to-date
  • Source: - https://cutadapt.readthedocs.org/en/stable/
  • ToolShed categories: - Fasta Manipulation, Fastq Manipulation, Sequence Analysis
  • ToolShed - id: cutadapt
  • Date of first commit of the suite: - 2023-11-03
  • Galaxy wrapper owner: lparsons
  • Galaxy - wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt
  • Galaxy - wrapper version: 4.9
  • Conda id: cutadapt
  • Conda - version: 4.9
  • EDAM operation (no superclasses): Sequence - trimming, Primer removal, Read pre-processing
  • EDAM topic (no superclasses): - Genomics, Probes and primers, Sequencing
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 259754
  • No. of tool users (all time) (usegalaxy.eu): 272370
  • Tool - usage (5 years) (usegalaxy.eu): 11716
  • Tool usage (all time) - (usegalaxy.eu): 12601
  • No. of tool users (5 years) (usegalaxy.org): - 334550
  • No. of tool users (all time) (usegalaxy.org): 362356
  • Tool - usage (5 years) (usegalaxy.org): 18618
  • Tool usage (all - time) (usegalaxy.org): 20162
  • No. of tool users (5 years) - (usegalaxy.org.au): 64377
  • No. of tool users (all time) - (usegalaxy.org.au): 65986
  • Tool usage (5 years) (usegalaxy.org.au): - 3507
  • Tool usage (all time) (usegalaxy.org.au): 3627
  • No. - of tool users (5 years) - all main servers: 658681
  • No. - of tool users (all time) - all main servers: 700712
  • Tool - usage (5 years) - all main servers: 33841
  • Tool usage (all - time) - all main servers: 36390
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Flexible tool to remove adapter sequences (and quality trim) high + throughput sequencing reads (fasta/fastq). title_md: cutadapt - - description_md: '
  • Galaxy tool ids: dada2_assignTaxonomyAddspecies, - dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, - dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, - dada2_seqCounts
  • Description: DADA2 wrappers
  • bio.tool - id: dada2
  • bio.tool ids: dada2
  • biii: - nan
  • bio.tool name: dada2
  • 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.
  • EDAM - operation: Variant calling, DNA barcoding
  • EDAM topic: - Sequencing, Genetic variation, Microbial ecology, Metagenomics
  • Status: - To update
  • Source: https://benjjneb.github.io/dada2/index.html
  • ToolShed - categories: Metagenomics
  • ToolShed id: dada2
  • Date - of first commit of the suite: 2019-07-05
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2
  • Galaxy - wrapper version: nan
  • Conda id: bioconductor-dada2
  • Conda - version: 1.30.0
  • EDAM operation (no superclasses): - Variant calling, DNA barcoding
  • EDAM topic (no superclasses): - Sequencing, Genetic variation, Microbial ecology, Metagenomics
  • Available - on UseGalaxy.org (Main): 10
  • Available on UseGalaxy.org.au: - 10
  • Available on UseGalaxy.eu: 10
  • Available - on UseGalaxy.fr: 10
  • Tools available on UseGalaxy.org (Main): - 10
  • Tools available on UseGalaxy.org.au: 10
  • Tools - available on UseGalaxy.eu: 10
  • Tools available on UseGalaxy.fr: - 10
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 10
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 92240
  • No. of tool - users (all time) (usegalaxy.eu): 92240
  • Tool usage (5 years) - (usegalaxy.eu): 2716
  • Tool usage (all time) (usegalaxy.eu): - 2716
  • No. of tool users (5 years) (usegalaxy.org): 179176
  • No. - of tool users (all time) (usegalaxy.org): 179176
  • Tool usage - (5 years) (usegalaxy.org): 5317
  • Tool usage (all time) (usegalaxy.org): - 5317
  • No. of tool users (5 years) (usegalaxy.org.au): 12478
  • No. - of tool users (all time) (usegalaxy.org.au): 12478
  • Tool - usage (5 years) (usegalaxy.org.au): 394
  • Tool usage (all - time) (usegalaxy.org.au): 394
  • No. of tool users (5 years) - - all main servers: 283894
  • No. of tool users (all time) - - all main servers: 283894
  • Tool usage (5 years) - all main - servers: 8427
  • Tool usage (all time) - all main servers: - 8427
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: DADA2 wrappers title_md: dada2 - - description_md: '
  • Galaxy tool ids: Fasta_to_Contig2Bin, das_tool
  • Description: - DAS Tool for genome resolved metagenomics
  • bio.tool id: - dastool
  • bio.tool ids: dastool
  • biii: - nan
  • bio.tool name: dastool
  • 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.
  • EDAM operation: Read binning
  • EDAM - topic: Metagenomics
  • Status: Up-to-date
  • Source: - https://github.com/cmks/DAS_Tool
  • ToolShed categories: Metagenomics
  • ToolShed - id: das_tool
  • Date of first commit of the suite: - 2022-06-23
  • Galaxy wrapper owner: iuc
  • Galaxy - wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool
  • Galaxy - wrapper version: 1.1.7
  • Conda id: das_tool
  • Conda - version: 1.1.7
  • EDAM operation (no superclasses): - Read binning
  • EDAM topic (no superclasses): Metagenomics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1323
  • No. of tool - users (all time) (usegalaxy.eu): 1323
  • Tool usage (5 years) - (usegalaxy.eu): 47
  • Tool usage (all time) (usegalaxy.eu): - 47
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1323
  • No. - of tool users (all time) - all main servers: 1323
  • Tool - usage (5 years) - all main servers: 47
  • Tool usage (all - time) - all main servers: 47
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: DAS Tool for genome resolved metagenomics title_md: das_tool - - description_md: '
  • Galaxy tool ids: deseq2
  • Description: - Differential gene expression analysis based on the negative binomial distribution
  • bio.tool - id: DESeq2
  • bio.tool ids: DESeq2
  • biii: - nan
  • bio.tool name: DESeq2
  • 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.
  • EDAM - operation: Differential gene expression analysis, RNA-Seq analysis
  • EDAM - topic: RNA-Seq
  • Status: To update
  • Source: - https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
  • ToolShed - categories: Transcriptomics, RNA, Statistics
  • ToolShed id: - deseq2
  • Date of first commit of the suite: 2018-11-15
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2
  • Galaxy - wrapper version: 2.11.40.8
  • Conda id: bioconductor-deseq2
  • Conda - version: 1.42.0
  • EDAM operation (no superclasses): - Differential gene expression analysis, RNA-Seq analysis
  • EDAM topic - (no superclasses): RNA-Seq
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 97434
  • No. of tool users (all time) (usegalaxy.eu): 109474
  • Tool - usage (5 years) (usegalaxy.eu): 11355
  • Tool usage (all time) - (usegalaxy.eu): 12514
  • No. of tool users (5 years) (usegalaxy.org): - 183905
  • No. of tool users (all time) (usegalaxy.org): 246475
  • Tool - usage (5 years) (usegalaxy.org): 24951
  • Tool usage (all - time) (usegalaxy.org): 31957
  • No. of tool users (5 years) - (usegalaxy.org.au): 18551
  • No. of tool users (all time) - (usegalaxy.org.au): 20166
  • Tool usage (5 years) (usegalaxy.org.au): - 2647
  • Tool usage (all time) (usegalaxy.org.au): 2905
  • No. - of tool users (5 years) - all main servers: 299890
  • No. - of tool users (all time) - all main servers: 376115
  • Tool - usage (5 years) - all main servers: 38953
  • Tool usage (all - time) - all main servers: 47376
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Differential gene expression analysis based on the negative binomial + distribution title_md: deseq2 - - description_md: '
  • Galaxy tool ids: bg_diamond, bg_diamond_makedb, - bg_diamond_view
  • Description: DIAMOND is a new alignment - tool for aligning short DNA sequencing reads to a protein reference database - such as NCBI-NR.
  • bio.tool id: diamond
  • bio.tool - ids: diamond
  • biii: nan
  • bio.tool name: - Diamond
  • 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.
  • EDAM operation: - Sequence alignment analysis
  • EDAM topic: Sequence analysis, - Proteins
  • Status: To update
  • Source: - https://github.com/bbuchfink/diamond
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: diamond
  • Date - of first commit of the suite: 2021-03-21
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond
  • Galaxy - wrapper version: 2.0.15
  • Conda id: diamond
  • Conda - version: 2.1.10
  • EDAM operation (no superclasses): - Sequence alignment analysis
  • EDAM topic (no superclasses): - Sequence analysis, Proteins
  • Available on UseGalaxy.org (Main): - 3
  • Available on UseGalaxy.org.au: 3
  • Available - on UseGalaxy.eu: 3
  • Available on UseGalaxy.fr: 3
  • Tools - available on UseGalaxy.org (Main): 3
  • Tools available on - UseGalaxy.org.au: 3
  • Tools available on UseGalaxy.eu: - 3
  • Tools available on UseGalaxy.fr: 3
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 61376
  • No. of tool users (all time) (usegalaxy.eu): 61746
  • Tool - usage (5 years) (usegalaxy.eu): 1847
  • Tool usage (all time) - (usegalaxy.eu): 1895
  • No. of tool users (5 years) (usegalaxy.org): - 23164
  • No. of tool users (all time) (usegalaxy.org): 28729
  • Tool - usage (5 years) (usegalaxy.org): 1140
  • Tool usage (all time) - (usegalaxy.org): 1556
  • No. of tool users (5 years) (usegalaxy.org.au): - 63034
  • No. of tool users (all time) (usegalaxy.org.au): - 63034
  • Tool usage (5 years) (usegalaxy.org.au): 522
  • Tool - usage (all time) (usegalaxy.org.au): 522
  • No. of tool users - (5 years) - all main servers: 147574
  • No. of tool users - (all time) - all main servers: 153509
  • Tool usage (5 years) - - all main servers: 3509
  • Tool usage (all time) - all main - servers: 3973
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: DIAMOND is a new alignment tool for aligning short DNA sequencing + reads to a protein reference database such as NCBI-NR. title_md: diamond - - description_md: '
  • Galaxy tool ids: disco
  • Description: - DISCO is a overlap-layout-consensus (OLC) metagenome assembler
  • bio.tool - id: disco
  • bio.tool ids: disco
  • biii: - nan
  • bio.tool name: DISCO
  • 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.
  • EDAM operation: Protein sequence - analysis
  • EDAM topic: Structure determination
  • Status: - To update
  • Source: http://disco.omicsbio.org/
  • ToolShed - categories: Metagenomics, Assembly
  • ToolShed id: - disco
  • Date of first commit of the suite: 2017-10-26
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco
  • Galaxy - wrapper version: nan
  • Conda id: disco
  • Conda - version: 1.2
  • EDAM operation (no superclasses): Protein - sequence analysis
  • EDAM topic (no superclasses): Structure - determination
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 358
  • No. of tool - users (all time) (usegalaxy.eu): 406
  • Tool usage (5 years) - (usegalaxy.eu): 124
  • Tool usage (all time) (usegalaxy.eu): - 139
  • No. of tool users (5 years) (usegalaxy.org): 1361
  • No. - of tool users (all time) (usegalaxy.org): 1361
  • Tool usage - (5 years) (usegalaxy.org): 384
  • Tool usage (all time) (usegalaxy.org): - 384
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1719
  • No. - of tool users (all time) - all main servers: 1767
  • Tool - usage (5 years) - all main servers: 508
  • Tool usage (all - time) - all main servers: 523
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: DISCO is a overlap-layout-consensus (OLC) metagenome assembler title_md: disco - - description_md: '
  • Galaxy tool ids: dram_annotate, dram_distill, - dram_merge_annotations, dram_neighborhoods, dram_strainer
  • Description: - DRAM for distilling microbial metabolism to automate the curation of microbiome - function
  • bio.tool id: dram
  • bio.tool ids: - dram
  • biii: nan
  • bio.tool name: DRAM
  • bio.tool - description: Distilled and Refined Annotation of Metabolism: A tool for - the annotation and curation of function for microbial and viral genomes
  • EDAM - operation: Gene functional annotation
  • EDAM topic: - Metagenomics, Biological databases, Molecular genetics
  • Status: - Up-to-date
  • Source: https://github.com/WrightonLabCSU/DRAM
  • ToolShed - categories: Metagenomics
  • ToolShed id: dram
  • Date - of first commit of the suite: 2022-09-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram
  • Galaxy - wrapper version: 1.5.0
  • Conda id: dram
  • Conda - version: 1.5.0
  • EDAM operation (no superclasses): - Gene functional annotation
  • EDAM topic (no superclasses): - Metagenomics, Biological databases, Molecular genetics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 5
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 7358
  • No. of tool - users (all time) (usegalaxy.eu): 7358
  • Tool usage (5 years) - (usegalaxy.eu): 88
  • Tool usage (all time) (usegalaxy.eu): - 88
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 7358
  • No. - of tool users (all time) - all main servers: 7358
  • Tool - usage (5 years) - all main servers: 88
  • Tool usage (all - time) - all main servers: 88
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: DRAM for distilling microbial metabolism to automate the curation + of microbiome function title_md: dram - - description_md: '
  • Galaxy tool ids: drep_compare, drep_dereplicate
  • Description: - dRep compares and dereplicates genome sets
  • bio.tool id: - drep
  • bio.tool ids: drep
  • biii: nan
  • bio.tool - name: dRep
  • bio.tool description: Fast and accurate - genomic comparisons that enables improved genome recovery from metagenomes through - de-replication.
  • EDAM operation: Genome comparison
  • EDAM - topic: Metagenomics, Genomics, Sequence analysis
  • Status: - Up-to-date
  • Source: https://github.com/MrOlm/drep
  • ToolShed - categories: Metagenomics
  • ToolShed id: drep
  • Date - of first commit of the suite: 2020-01-06
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep
  • Galaxy - wrapper version: 3.5.0
  • Conda id: drep
  • Conda - version: 3.5.0
  • EDAM operation (no superclasses): - Genome comparison
  • EDAM topic (no superclasses): Metagenomics, - Sequence analysis
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 2
  • Available on UseGalaxy.fr: 2
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 2
  • Tools - available on UseGalaxy.fr: 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: - 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 916
  • No. of tool - users (all time) (usegalaxy.eu): 916
  • Tool usage (5 years) - (usegalaxy.eu): 113
  • Tool usage (all time) (usegalaxy.eu): - 113
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 916
  • No. - of tool users (all time) - all main servers: 916
  • Tool usage - (5 years) - all main servers: 113
  • Tool usage (all time) - - all main servers: 113
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: dRep compares and dereplicates genome sets title_md: drep - - description_md: '
  • Galaxy tool ids: ectyper
  • Description: - EC-Typer - in silico serotyping of Escherichia coli species
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: Up-to-date
  • Source: https://github.com/phac-nml/ecoli_serotyping
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: ectyper
  • Date - of first commit of the suite: 2018-12-21
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/ecoli_serotyping
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper
  • Galaxy - wrapper version: 1.0.0
  • Conda id: ectyper
  • Conda - version: 1.0.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 12996
  • No. of tool - users (all time) (usegalaxy.eu): 12996
  • Tool usage (5 years) - (usegalaxy.eu): 137
  • Tool usage (all time) (usegalaxy.eu): - 137
  • No. of tool users (5 years) (usegalaxy.org): 10
  • No. - of tool users (all time) (usegalaxy.org): 10
  • Tool usage - (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): - 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 13006
  • No. - of tool users (all time) - all main servers: 13006
  • Tool - usage (5 years) - all main servers: 138
  • Tool usage (all - time) - all main servers: 138
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: EC-Typer - in silico serotyping of Escherichia coli species title_md: ectyper - - description_md: '
  • Galaxy tool ids: effectiveT3
  • Description: - Find bacterial type III effectors in protein sequences
  • bio.tool - id: effectivet3
  • bio.tool ids: effectivet3
  • biii: - nan
  • bio.tool name: EffectiveT3
  • bio.tool description: - Prediction of putative Type-III secreted proteins.
  • EDAM operation: - Sequence classification
  • EDAM topic: Sequence analysis
  • Status: - To update
  • Source: http://effectors.org
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: effectivet3
  • Date - of first commit of the suite: 2015-09-21
  • Galaxy wrapper - owner: peterjc
  • Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
  • Galaxy - wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
  • Galaxy - wrapper version: 0.0.21
  • Conda id: effectiveT3
  • Conda - version: 1.0.1
  • EDAM operation (no superclasses): - Sequence classification
  • EDAM topic (no superclasses): Sequence - analysis
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 0
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 0
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Find bacterial type III effectors in protein sequences title_md: effectiveT3 - - description_md: '
  • Galaxy tool ids: eggnog_mapper, eggnog_mapper_annotate, - eggnog_mapper_search
  • Description: eggnog-mapper fast functional - annotation of novel sequences
  • bio.tool id: eggnog-mapper-v2
  • bio.tool - ids: eggnog-mapper-v2
  • biii: nan
  • bio.tool - name: eggNOG-mapper v2
  • bio.tool description: EggNOG-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.
  • EDAM - operation: Homology-based gene prediction, Genome annotation, Fold recognition, - Information extraction, Query and retrieval
  • EDAM topic: - Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis
  • Status: - To update
  • Source: nan
  • ToolShed categories: - Proteomics
  • ToolShed id: eggnog_mapper
  • Date - of first commit of the suite: 2019-11-11
  • Galaxy wrapper - owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper
  • Galaxy - wrapper version: 2.1.8
  • Conda id: eggnog-mapper
  • Conda - version: 2.1.12
  • EDAM operation (no superclasses): - Homology-based gene prediction, Genome annotation, Fold recognition, Information - extraction, Query and retrieval
  • EDAM topic (no superclasses): - Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis
  • Available - on UseGalaxy.org (Main): 3
  • Available on UseGalaxy.org.au: - 3
  • Available on UseGalaxy.eu: 3
  • Available - on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): - 3
  • Tools available on UseGalaxy.org.au: 3
  • Tools - available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: - 3
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 3
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 3
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 34432
  • No. of tool - users (all time) (usegalaxy.eu): 34437
  • Tool usage (5 years) - (usegalaxy.eu): 1149
  • Tool usage (all time) (usegalaxy.eu): - 1152
  • No. of tool users (5 years) (usegalaxy.org): 42
  • No. - of tool users (all time) (usegalaxy.org): 42
  • Tool usage - (5 years) (usegalaxy.org): 2
  • Tool usage (all time) (usegalaxy.org): - 2
  • No. of tool users (5 years) (usegalaxy.org.au): 21027
  • No. - of tool users (all time) (usegalaxy.org.au): 21027
  • Tool - usage (5 years) (usegalaxy.org.au): 413
  • Tool usage (all - time) (usegalaxy.org.au): 413
  • No. of tool users (5 years) - - all main servers: 55501
  • No. of tool users (all time) - - all main servers: 55506
  • Tool usage (5 years) - all main - servers: 1564
  • Tool usage (all time) - all main servers: - 1567
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: eggnog-mapper fast functional annotation of novel sequences title_md: eggnog_mapper - - description_md: '
  • 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
  • Description: - Galaxy wrappers for EMBOSS version 5.0.0 tools
  • bio.tool id: - emboss
  • bio.tool ids: emboss
  • biii: - nan
  • bio.tool name: EMBOSS
  • bio.tool description: - Diverse suite of tools for sequence analysis; many programs analagous to GCG; - context-sensitive help for each tool.
  • EDAM operation: Sequence - analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence - alignment
  • EDAM topic: Molecular biology, Sequence analysis, - Biology
  • Status: To update
  • Source: - http://emboss.open-bio.org/
  • ToolShed categories: Sequence - Analysis, Fasta Manipulation
  • ToolShed id: emboss_5
  • Date - of first commit of the suite: 2017-01-11
  • Galaxy wrapper - owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5
  • Galaxy - wrapper version: 5.0.0
  • Conda id: emboss
  • Conda - version: 6.6.0
  • EDAM operation (no superclasses): - Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, - Sequence alignment
  • EDAM topic (no superclasses): Molecular - biology, Sequence analysis
  • Available on UseGalaxy.org (Main): - 107
  • Available on UseGalaxy.org.au: 107
  • Available - on UseGalaxy.eu: 107
  • Available on UseGalaxy.fr: - 107
  • Tools available on UseGalaxy.org (Main): 107
  • Tools - available on UseGalaxy.org.au: 107
  • Tools available on UseGalaxy.eu: - 107
  • Tools available on UseGalaxy.fr: 107
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 107
  • Tools available on Viral - Variant Visualizer (VVV): 0
  • No. of tool users (5 years) - (usegalaxy.eu): 143762
  • No. of tool users (all time) (usegalaxy.eu): - 148864
  • Tool usage (5 years) (usegalaxy.eu): 4481
  • Tool - usage (all time) (usegalaxy.eu): 5039
  • No. of tool users - (5 years) (usegalaxy.org): 151989
  • No. of tool users (all - time) (usegalaxy.org): 296028
  • Tool usage (5 years) (usegalaxy.org): - 13224
  • Tool usage (all time) (usegalaxy.org): 31140
  • No. - of tool users (5 years) (usegalaxy.org.au): 24955
  • No. of - tool users (all time) (usegalaxy.org.au): 27001
  • Tool usage - (5 years) (usegalaxy.org.au): 2397
  • Tool usage (all time) - (usegalaxy.org.au): 2705
  • No. of tool users (5 years) - - all main servers: 320706
  • No. of tool users (all time) - - all main servers: 471893
  • Tool usage (5 years) - all main - servers: 20102
  • Tool usage (all time) - all main servers: - 38884
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Galaxy wrappers for EMBOSS version 5.0.0 tools title_md: emboss_5 - - description_md: '
  • 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
  • Description: - Analyse phylogenetic trees using the ETE Toolkit
  • bio.tool id: - ete
  • bio.tool ids: ete
  • biii: nan
  • bio.tool - name: ete
  • 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
  • EDAM operation: - Phylogenetic analysis, Phylogenetic tree editing
  • EDAM topic: - Phylogenetics
  • Status: To update
  • Source: - http://etetoolkit.org/
  • ToolShed categories: Phylogenetics
  • ToolShed - id: ete
  • Date of first commit of the suite: 2018-10-11
  • Galaxy - wrapper owner: earlhaminst
  • Galaxy wrapper source: - https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete
  • Galaxy - wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete
  • Galaxy - wrapper version: 3.1.2
  • Conda id: ete3
  • Conda - version: 3.1.1
  • EDAM operation (no superclasses): - Phylogenetic tree editing
  • EDAM topic (no superclasses): - Phylogenetics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 7
  • Available on UseGalaxy.fr: 7
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 7
  • Tools - available on UseGalaxy.fr: 7
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 7
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 820
  • No. of tool - users (all time) (usegalaxy.eu): 966
  • Tool usage (5 years) - (usegalaxy.eu): 89
  • Tool usage (all time) (usegalaxy.eu): - 106
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 820
  • No. - of tool users (all time) - all main servers: 966
  • Tool usage - (5 years) - all main servers: 89
  • Tool usage (all time) - - all main servers: 106
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Analyse phylogenetic trees using the ETE Toolkit title_md: ete - - description_md: '
  • Galaxy tool ids: export2graphlan
  • Description: - export2graphlan is a conversion software tool for producing both annotation - and tree file for GraPhlAn
  • bio.tool id: export2graphlan
  • bio.tool - ids: export2graphlan
  • biii: nan
  • bio.tool - name: export2graphlan
  • 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.
  • EDAM - operation: Conversion
  • EDAM topic: Taxonomy, Metabolomics, - Biomarkers
  • Status: To update
  • Source: - https://bitbucket.org/CibioCM/export2graphlan/overview
  • ToolShed - categories: Metagenomics
  • ToolShed id: export2graphlan
  • Date - of first commit of the suite: 2017-03-03
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan
  • Galaxy - wrapper version: 0.20
  • Conda id: export2graphlan
  • Conda - version: 0.22
  • EDAM operation (no superclasses): - Conversion
  • EDAM topic (no superclasses): Taxonomy, Metabolomics, - Biomarkers
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 5396
  • No. of tool - users (all time) (usegalaxy.eu): 5938
  • Tool usage (5 years) - (usegalaxy.eu): 580
  • Tool usage (all time) (usegalaxy.eu): - 607
  • No. of tool users (5 years) (usegalaxy.org): 628
  • No. - of tool users (all time) (usegalaxy.org): 628
  • Tool usage - (5 years) (usegalaxy.org): 168
  • Tool usage (all time) (usegalaxy.org): - 168
  • No. of tool users (5 years) (usegalaxy.org.au): 519
  • No. - of tool users (all time) (usegalaxy.org.au): 519
  • Tool usage - (5 years) (usegalaxy.org.au): 107
  • Tool usage (all time) - (usegalaxy.org.au): 107
  • No. of tool users (5 years) - all - main servers: 6543
  • No. of tool users (all time) - all main - servers: 7085
  • Tool usage (5 years) - all main servers: - 855
  • Tool usage (all time) - all main servers: 882
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: export2graphlan is a conversion software tool for producing both + annotation and tree file for GraPhlAn title_md: export2graphlan - - description_md: '
  • Galaxy tool ids: ez_histograms
  • Description: - ggplot2 histograms and density plots
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://github.com/tidyverse/ggplot2
  • ToolShed categories: - Visualization, Statistics
  • ToolShed id: ez_histograms
  • Date - of first commit of the suite: 2024-02-07
  • Galaxy wrapper - owner: artbio
  • Galaxy wrapper source: https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms
  • Galaxy - wrapper parsed folder: https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms
  • Galaxy - wrapper version: 3.4.4
  • Conda id: r-ggplot2
  • Conda - version: 2.2.1
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: ggplot2 histograms and density plots title_md: ez_histograms - - description_md: '
  • Galaxy tool ids: fargene
  • Description: - fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )
  • bio.tool - id: fargene
  • bio.tool ids: fargene
  • biii: - nan
  • bio.tool name: fARGene
  • 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.
  • EDAM - operation: Antimicrobial resistance prediction
  • EDAM topic: - Metagenomics, Microbiology, Public health and epidemiology
  • Status: - Up-to-date
  • Source: https://github.com/fannyhb/fargene
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: fargene
  • Date - of first commit of the suite: 2019-08-30
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene
  • Galaxy - wrapper version: 0.1
  • Conda id: fargene
  • Conda - version: 0.1
  • EDAM operation (no superclasses): Antimicrobial - resistance prediction
  • EDAM topic (no superclasses): Metagenomics, - Microbiology, Public health and epidemiology
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 601
  • No. of tool users (all time) (usegalaxy.eu): 601
  • Tool - usage (5 years) (usegalaxy.eu): 128
  • Tool usage (all time) - (usegalaxy.eu): 128
  • No. of tool users (5 years) (usegalaxy.org): - 1165
  • No. of tool users (all time) (usegalaxy.org): 1165
  • Tool - usage (5 years) (usegalaxy.org): 232
  • Tool usage (all time) - (usegalaxy.org): 232
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 1766
  • No. of tool users (all time) - all main - servers: 1766
  • Tool usage (5 years) - all main servers: - 360
  • Tool usage (all time) - all main servers: 360
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) title_md: fargene - - description_md: '
  • Galaxy tool ids: fastani
  • Description: - Fast alignment-free computation of whole-genome Average Nucleotide Identity
  • bio.tool - id: fastani
  • bio.tool ids: fastani
  • biii: - nan
  • bio.tool name: FastANI
  • 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.
  • EDAM operation: - Genome alignment, Sequence similarity search
  • EDAM topic: - Microbiology, Genetic variation
  • Status: To update
  • Source: - https://github.com/ParBLiSS/FastANI
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: fastani
  • Date - of first commit of the suite: 2020-02-17
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani
  • Galaxy - wrapper version: 1.3
  • Conda id: fastani
  • Conda - version: 1.34
  • EDAM operation (no superclasses): - Genome alignment, Sequence similarity search
  • EDAM topic (no superclasses): - Microbiology, Genetic variation
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 6685
  • No. of tool users (all time) (usegalaxy.eu): 6685
  • Tool - usage (5 years) (usegalaxy.eu): 603
  • Tool usage (all time) - (usegalaxy.eu): 603
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 6685
  • No. of tool users (all time) - all main - servers: 6685
  • Tool usage (5 years) - all main servers: - 603
  • Tool usage (all time) - all main servers: 603
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Fast alignment-free computation of whole-genome Average Nucleotide + Identity title_md: fastani - - description_md: '
  • Galaxy tool ids: fastk_fastk
  • Description: - FastK: A K-mer counter (for HQ assembly data sets)
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: https://github.com/thegenemyers/FASTK
  • ToolShed - categories: Assembly
  • ToolShed id: fastk
  • Date - of first commit of the suite: 2024-05-03
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk
  • Galaxy - wrapper version: 1.0.0
  • Conda id: fastk
  • Conda - version: 1.0
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 136
  • No. of tool users (all time) (usegalaxy.eu): 136
  • Tool - usage (5 years) (usegalaxy.eu): 11
  • Tool usage (all time) - (usegalaxy.eu): 11
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 136
  • No. of tool users (all time) - all main - servers: 136
  • Tool usage (5 years) - all main servers: - 11
  • Tool usage (all time) - all main servers: 11
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: 'FastK: A K-mer counter (for HQ assembly data sets)' title_md: fastk - - description_md: '
  • Galaxy tool ids: fastp
  • Description: - Fast all-in-one preprocessing for FASTQ files
  • bio.tool id: - fastp
  • bio.tool ids: fastp
  • biii: nan
  • bio.tool - name: fastp
  • 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.
  • EDAM - operation: Sequencing quality control, Sequence contamination filtering
  • EDAM - topic: Sequence analysis, Probes and primers
  • Status: - Up-to-date
  • Source: https://github.com/OpenGene/fastp
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: fastp
  • Date - of first commit of the suite: 2018-03-18
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp
  • Galaxy - wrapper version: 0.23.4
  • Conda id: fastp
  • Conda - version: 0.23.4
  • EDAM operation (no superclasses): - Sequence contamination filtering
  • EDAM topic (no superclasses): - Probes and primers
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 1
  • No. - of tool users (5 years) (usegalaxy.eu): 1126086
  • No. of - tool users (all time) (usegalaxy.eu): 1127111
  • Tool usage - (5 years) (usegalaxy.eu): 6847
  • Tool usage (all time) (usegalaxy.eu): - 6909
  • No. of tool users (5 years) (usegalaxy.org): 422259
  • No. - of tool users (all time) (usegalaxy.org): 422259
  • Tool usage - (5 years) (usegalaxy.org): 10722
  • Tool usage (all time) - (usegalaxy.org): 10722
  • No. of tool users (5 years) (usegalaxy.org.au): - 76462
  • No. of tool users (all time) (usegalaxy.org.au): - 76462
  • Tool usage (5 years) (usegalaxy.org.au): 2242
  • Tool - usage (all time) (usegalaxy.org.au): 2242
  • No. of tool users - (5 years) - all main servers: 1624807
  • No. of tool users - (all time) - all main servers: 1625832
  • Tool usage (5 years) - - all main servers: 19811
  • Tool usage (all time) - all main - servers: 19873
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: Fast all-in-one preprocessing for FASTQ files title_md: fastp - - description_md: '
  • Galaxy tool ids: fastqe
  • Description: - FASTQE
  • bio.tool id: fastqe
  • bio.tool ids: - fastqe
  • biii: nan
  • bio.tool name: FASTQE
  • bio.tool - description: Compute quality stats for FASTQ files and print those stats - as emoji... for some reason.
  • EDAM operation: Sequencing - quality control
  • EDAM topic: Sequence analysis, Sequencing
  • Status: - To update
  • Source: https://fastqe.com/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: fastqe
  • Date - of first commit of the suite: 2020-07-13
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe
  • Galaxy - wrapper version: 0.3.1+galaxy0
  • Conda id: fastqe
  • Conda - version: 0.3.1
  • EDAM operation (no superclasses): - Sequencing quality control
  • EDAM topic (no superclasses): - Sequence analysis, Sequencing
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 5162
  • No. of tool users (all time) (usegalaxy.eu): 5162
  • Tool - usage (5 years) (usegalaxy.eu): 2350
  • Tool usage (all time) - (usegalaxy.eu): 2350
  • No. of tool users (5 years) (usegalaxy.org): - 10176
  • No. of tool users (all time) (usegalaxy.org): 10176
  • Tool - usage (5 years) (usegalaxy.org): 4714
  • Tool usage (all time) - (usegalaxy.org): 4714
  • No. of tool users (5 years) (usegalaxy.org.au): - 2610
  • No. of tool users (all time) (usegalaxy.org.au): 2610
  • Tool - usage (5 years) (usegalaxy.org.au): 991
  • Tool usage (all - time) (usegalaxy.org.au): 991
  • No. of tool users (5 years) - - all main servers: 17948
  • No. of tool users (all time) - - all main servers: 17948
  • Tool usage (5 years) - all main - servers: 8055
  • Tool usage (all time) - all main servers: - 8055
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: FASTQE title_md: fastqe - - description_md: '
  • Galaxy tool ids: fasttree
  • Description: - FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments - of nucleotide or protein sequences - GVL
  • bio.tool id: fasttree
  • bio.tool - ids: fasttree
  • biii: nan
  • bio.tool name: - FastTree
  • bio.tool description: Infers approximately-maximum-likelihood - phylogenetic trees from alignments of nucleotide or protein sequences.
  • EDAM - operation: Phylogenetic tree generation (from molecular sequences), Phylogenetic - tree generation (maximum likelihood and Bayesian methods)
  • EDAM - topic: Phylogenetics, Sequence analysis
  • Status: - To update
  • Source: http://www.microbesonline.org/fasttree/
  • ToolShed - categories: Phylogenetics
  • ToolShed id: fasttree
  • Date - of first commit of the suite: 2018-02-02
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree
  • Galaxy - wrapper version: 2.1.10
  • Conda id: fasttree
  • Conda - version: 2.1.11
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): Phylogenetics
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 65542
  • No. of tool - users (all time) (usegalaxy.eu): 65631
  • Tool usage (5 years) - (usegalaxy.eu): 1049
  • Tool usage (all time) (usegalaxy.eu): - 1071
  • No. of tool users (5 years) (usegalaxy.org): 25992
  • No. - of tool users (all time) (usegalaxy.org): 25992
  • Tool usage - (5 years) (usegalaxy.org): 2147
  • Tool usage (all time) (usegalaxy.org): - 2147
  • No. of tool users (5 years) (usegalaxy.org.au): 6733
  • No. - of tool users (all time) (usegalaxy.org.au): 7339
  • Tool - usage (5 years) (usegalaxy.org.au): 649
  • Tool usage (all - time) (usegalaxy.org.au): 745
  • No. of tool users (5 years) - - all main servers: 98267
  • No. of tool users (all time) - - all main servers: 98962
  • Tool usage (5 years) - all main - servers: 3845
  • Tool usage (all time) - all main servers: - 3963
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: FastTree infers approximately-maximum-likelihood phylogenetic + trees from alignments of nucleotide or protein sequences - GVL title_md: fasttree - - description_md: '
  • Galaxy tool ids: featurecounts
  • Description: - featureCounts counts the number of reads aligned to defined masked regions in - a reference genome
  • bio.tool id: featurecounts
  • bio.tool - ids: featurecounts
  • biii: nan
  • bio.tool - name: FeatureCounts
  • 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.
  • EDAM operation: - Read summarisation, RNA-Seq quantification
  • EDAM topic: - RNA-Seq
  • Status: To update
  • Source: - http://bioinf.wehi.edu.au/featureCounts
  • ToolShed categories: - RNA, Transcriptomics, Sequence Analysis
  • ToolShed id: featurecounts
  • Date - of first commit of the suite: 2019-05-28
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts
  • Galaxy - wrapper version: 2.0.3
  • Conda id: subread
  • Conda - version: 2.0.6
  • EDAM operation (no superclasses): - Read summarisation, RNA-Seq quantification
  • EDAM topic (no superclasses): - RNA-Seq
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 740719
  • No. of tool - users (all time) (usegalaxy.eu): 770524
  • Tool usage (5 years) - (usegalaxy.eu): 11699
  • Tool usage (all time) (usegalaxy.eu): - 12547
  • No. of tool users (5 years) (usegalaxy.org): 643892
  • No. - of tool users (all time) (usegalaxy.org): 784396
  • Tool usage - (5 years) (usegalaxy.org): 23272
  • Tool usage (all time) - (usegalaxy.org): 27598
  • No. of tool users (5 years) (usegalaxy.org.au): - 66108
  • No. of tool users (all time) (usegalaxy.org.au): - 68867
  • Tool usage (5 years) (usegalaxy.org.au): 2348
  • Tool - usage (all time) (usegalaxy.org.au): 2463
  • No. of tool users - (5 years) - all main servers: 1450719
  • No. of tool users - (all time) - all main servers: 1623787
  • Tool usage (5 years) - - all main servers: 37319
  • Tool usage (all time) - all main - servers: 42608
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: featureCounts counts the number of reads aligned to defined masked + regions in a reference genome title_md: featurecounts - - description_md: '
  • Galaxy tool ids: filter_spades_repeat
  • Description: - Remove short and repeat contigs/scaffolds
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: https://github.com/phac-nml/galaxy_tools/
  • ToolShed - categories: Assembly
  • ToolShed id: filter_spades_repeats
  • Date - of first commit of the suite: 2017-10-12
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools/
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats
  • Galaxy - wrapper version: 1.0.1
  • Conda id: perl-bioperl
  • Conda - version: 1.7.8
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Remove short and repeat contigs/scaffolds title_md: filter_spades_repeats - - description_md: '
  • Galaxy tool ids: filtlong
  • Description: - Filtlong - Filtering long reads by quality
  • bio.tool id: - filtlong
  • bio.tool ids: filtlong
  • biii: - nan
  • bio.tool name: Filtlong
  • 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.
  • EDAM operation: Filtering, Sequencing quality - control
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: - https://github.com/rrwick/Filtlong
  • ToolShed categories: - Fastq Manipulation, Sequence Analysis
  • ToolShed id: filtlong
  • Date - of first commit of the suite: 2018-09-14
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong
  • Galaxy - wrapper version: 0.2.1
  • Conda id: filtlong
  • Conda - version: 0.2.1
  • EDAM operation (no superclasses): - Filtering, Sequencing quality control
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 53310
  • No. of tool - users (all time) (usegalaxy.eu): 53944
  • Tool usage (5 years) - (usegalaxy.eu): 1499
  • Tool usage (all time) (usegalaxy.eu): - 1575
  • No. of tool users (5 years) (usegalaxy.org): 25043
  • No. - of tool users (all time) (usegalaxy.org): 25043
  • Tool usage - (5 years) (usegalaxy.org): 726
  • Tool usage (all time) (usegalaxy.org): - 726
  • No. of tool users (5 years) (usegalaxy.org.au): 10824
  • No. - of tool users (all time) (usegalaxy.org.au): 10824
  • Tool - usage (5 years) (usegalaxy.org.au): 593
  • Tool usage (all - time) (usegalaxy.org.au): 593
  • No. of tool users (5 years) - - all main servers: 89177
  • No. of tool users (all time) - - all main servers: 89811
  • Tool usage (5 years) - all main - servers: 2818
  • Tool usage (all time) - all main servers: - 2894
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Filtlong - Filtering long reads by quality title_md: filtlong - - description_md: '
  • Galaxy tool ids: flashlfq
  • Description: - FlashLFQ mass-spectrometry proteomics label-free quantification
  • bio.tool - id: flashlfq
  • bio.tool ids: flashlfq
  • biii: - nan
  • bio.tool name: FlashLFQ
  • bio.tool description: - FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry - proteomics.
  • EDAM operation: Label-free quantification
  • EDAM - topic: Proteomics experiment, Proteomics
  • Status: - To update
  • Source: https://github.com/smith-chem-wisc/FlashLFQ
  • ToolShed - categories: Proteomics
  • ToolShed id: flashlfq
  • Date - of first commit of the suite: 2017-12-06
  • Galaxy wrapper - owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq
  • Galaxy - wrapper version: 1.0.3.1
  • Conda id: flashlfq
  • Conda - version: 1.2.6
  • EDAM operation (no superclasses): - Label-free quantification
  • EDAM topic (no superclasses): - Proteomics experiment, Proteomics
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 661
  • No. of tool users (all time) (usegalaxy.eu): 715
  • Tool - usage (5 years) (usegalaxy.eu): 52
  • Tool usage (all time) - (usegalaxy.eu): 54
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 167
  • No. of tool users (all time) (usegalaxy.org.au): 167
  • Tool - usage (5 years) (usegalaxy.org.au): 15
  • Tool usage (all - time) (usegalaxy.org.au): 15
  • No. of tool users (5 years) - - all main servers: 828
  • No. of tool users (all time) - - all main servers: 882
  • Tool usage (5 years) - all main servers: - 67
  • Tool usage (all time) - all main servers: 69
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: FlashLFQ mass-spectrometry proteomics label-free quantification title_md: flashlfq - - description_md: '
  • Galaxy tool ids: flye
  • Description: - Assembly of long and error-prone reads.
  • bio.tool id: Flye
  • bio.tool - ids: Flye
  • biii: nan
  • bio.tool name: - Flye
  • 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.
  • EDAM operation: Genome assembly, De-novo assembly, - Mapping assembly, Cross-assembly
  • EDAM topic: Sequence assembly, - Metagenomics, Whole genome sequencing, Genomics
  • Status: - Up-to-date
  • Source: https://github.com/fenderglass/Flye/
  • ToolShed - categories: Assembly
  • ToolShed id: flye
  • Date - of first commit of the suite: 2018-09-24
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/flye
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/flye
  • Galaxy - wrapper version: 2.9.5
  • Conda id: flye
  • Conda - version: 2.9.5
  • EDAM operation (no superclasses): - Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly
  • EDAM - topic (no superclasses): Sequence assembly, Metagenomics, Whole genome - sequencing
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 32514
  • No. of tool - users (all time) (usegalaxy.eu): 32675
  • Tool usage (5 years) - (usegalaxy.eu): 3379
  • Tool usage (all time) (usegalaxy.eu): - 3422
  • No. of tool users (5 years) (usegalaxy.org): 19434
  • No. - of tool users (all time) (usegalaxy.org): 19434
  • Tool usage - (5 years) (usegalaxy.org): 2537
  • Tool usage (all time) (usegalaxy.org): - 2537
  • No. of tool users (5 years) (usegalaxy.org.au): 9843
  • No. - of tool users (all time) (usegalaxy.org.au): 9843
  • Tool - usage (5 years) (usegalaxy.org.au): 1624
  • Tool usage (all - time) (usegalaxy.org.au): 1624
  • No. of tool users (5 years) - - all main servers: 61791
  • No. of tool users (all time) - - all main servers: 61952
  • Tool usage (5 years) - all main - servers: 7540
  • Tool usage (all time) - all main servers: - 7583
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Assembly of long and error-prone reads. title_md: flye - - description_md: '
  • Galaxy tool ids: format_metaphlan2_output
  • Description: - Format MetaPhlAn2 output to extract abundance at different taxonomic levels
  • bio.tool - id: format_metaphlan2_output
  • bio.tool ids: format_metaphlan2_output
  • biii: - nan
  • bio.tool name: Format metaphlan2 output
  • bio.tool - description: This tool format output file of MetaPhlan2 containing community - content (abundance) at all taxonomic levels (from kingdom to strains).
  • EDAM - operation: Formatting
  • EDAM topic: Taxonomy, Metagenomics
  • Status: - To update
  • Source: nan
  • ToolShed categories: - Metagenomics
  • ToolShed id: format_metaphlan2_output
  • Date - of first commit of the suite: 2022-10-19
  • Galaxy wrapper - owner: bebatut
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output
  • Galaxy - wrapper version: 0.2.0
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): Formatting
  • EDAM - topic (no superclasses): Taxonomy, Metagenomics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 5940
  • No. of tool - users (all time) (usegalaxy.eu): 6474
  • Tool usage (5 years) - (usegalaxy.eu): 558
  • Tool usage (all time) (usegalaxy.eu): - 608
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 5940
  • No. - of tool users (all time) - all main servers: 6474
  • Tool - usage (5 years) - all main servers: 558
  • Tool usage (all - time) - all main servers: 608
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Format MetaPhlAn2 output to extract abundance at different taxonomic + levels title_md: format_metaphlan2_output - - description_md: '
  • Galaxy tool ids: fraggenescan
  • Description: - Tool for finding (fragmented) genes in short read
  • bio.tool id: - fraggenescan
  • bio.tool ids: fraggenescan
  • biii: - nan
  • bio.tool name: FragGeneScan
  • bio.tool - description: Application for finding (fragmented) genes in short reads
  • EDAM - operation: Gene prediction
  • EDAM topic: Genetics, - Sequence analysis
  • Status: To update
  • Source: - https://sourceforge.net/projects/fraggenescan/
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: fraggenescan
  • Date - of first commit of the suite: 2017-09-04
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan
  • Galaxy - wrapper version: nan
  • Conda id: fraggenescan
  • Conda - version: 1.31
  • EDAM operation (no superclasses): - Gene prediction
  • EDAM topic (no superclasses): Genetics, - Sequence analysis
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1257
  • No. of tool - users (all time) (usegalaxy.eu): 1450
  • Tool usage (5 years) - (usegalaxy.eu): 150
  • Tool usage (all time) (usegalaxy.eu): - 162
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 1052
  • No. - of tool users (all time) (usegalaxy.org.au): 1052
  • Tool - usage (5 years) (usegalaxy.org.au): 45
  • Tool usage (all - time) (usegalaxy.org.au): 45
  • No. of tool users (5 years) - - all main servers: 2309
  • No. of tool users (all time) - - all main servers: 2502
  • Tool usage (5 years) - all main - servers: 195
  • Tool usage (all time) - all main servers: - 207
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Tool for finding (fragmented) genes in short read title_md: fraggenescan - - description_md: '
  • Galaxy tool ids: freyja_aggregate_plot, - freyja_boot, freyja_demix, freyja_variants
  • Description: - lineage abundances estimation
  • bio.tool id: freyja
  • bio.tool - ids: freyja
  • biii: nan
  • bio.tool name: - Freyja
  • bio.tool description: Recover relative lineage abundances - from mixed SARS-CoV-2 samples from a sequencing dataset
  • EDAM operation: - RNA-Seq quantification
  • EDAM topic: Metagenomics
  • Status: - Up-to-date
  • Source: https://github.com/andersen-lab/Freyja
  • ToolShed - categories: Metagenomics, Sequence Analysis
  • ToolShed id: - freyja
  • Date of first commit of the suite: 2022-07-05
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja
  • Galaxy - wrapper version: 1.5.1
  • Conda id: freyja
  • Conda - version: 1.5.1
  • EDAM operation (no superclasses): - RNA-Seq quantification
  • EDAM topic (no superclasses): Metagenomics
  • Available - on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 4
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 2
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 4
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 21757
  • No. of tool - users (all time) (usegalaxy.eu): 21757
  • Tool usage (5 years) - (usegalaxy.eu): 101
  • Tool usage (all time) (usegalaxy.eu): - 101
  • No. of tool users (5 years) (usegalaxy.org): 217
  • No. - of tool users (all time) (usegalaxy.org): 217
  • Tool usage - (5 years) (usegalaxy.org): 21
  • Tool usage (all time) (usegalaxy.org): - 21
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 21974
  • No. - of tool users (all time) - all main servers: 21974
  • Tool - usage (5 years) - all main servers: 122
  • Tool usage (all - time) - all main servers: 122
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: lineage abundances estimation title_md: freyja - - description_md: '
  • 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
  • Description: - Suite for metabarcoding analysis
  • bio.tool id: frogs
  • bio.tool - ids: frogs
  • biii: nan
  • bio.tool name: - FROGS
  • 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.
  • EDAM operation: - Taxonomic classification
  • EDAM topic: Metagenomics, Microbial - ecology, Taxonomy, Evolutionary biology, Sequencing
  • Status: - To update
  • Source: http://frogs.toulouse.inrae.fr/
  • ToolShed - categories: Metagenomics
  • ToolShed id: frogs
  • Date - of first commit of the suite: 2023-04-26
  • Galaxy wrapper - owner: frogs
  • Galaxy wrapper source: https://github.com/geraldinepascal/FROGS-wrappers/
  • Galaxy - wrapper parsed folder: https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs
  • Galaxy - wrapper version: 4.1.0
  • Conda id: frogs
  • Conda - version: 5.0.0
  • EDAM operation (no superclasses): - Taxonomic classification
  • EDAM topic (no superclasses): - Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 28
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 28
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Suite for metabarcoding analysis title_md: frogs - - description_md: '
  • Galaxy tool ids: funannotate_annotate, funannotate_clean, - funannotate_compare, funannotate_predict, funannotate_sort
  • Description: - Funannotate is a genome prediction, annotation, and comparison software package.
  • bio.tool - id: funannotate
  • bio.tool ids: funannotate
  • biii: - nan
  • bio.tool name: funannotate
  • bio.tool description: - funannotate is a pipeline for genome annotation (built specifically for fungi, - but will also work with higher eukaryotes).
  • EDAM operation: - Genome annotation
  • EDAM topic: Genomics
  • Status: - To update
  • Source: https://funannotate.readthedocs.io
  • ToolShed - categories: Genome annotation
  • ToolShed id: nan
  • Date - of first commit of the suite: 2021-08-26
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate
  • Galaxy - wrapper version: 1.8.15
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): Genome - annotation
  • EDAM topic (no superclasses): Genomics
  • Available - on UseGalaxy.org (Main): 3
  • Available on UseGalaxy.org.au: - 5
  • Available on UseGalaxy.eu: 5
  • Available - on UseGalaxy.fr: 5
  • Tools available on UseGalaxy.org (Main): - 3
  • Tools available on UseGalaxy.org.au: 5
  • Tools - available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: - 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 8648
  • No. of tool - users (all time) (usegalaxy.eu): 8648
  • Tool usage (5 years) - (usegalaxy.eu): 1408
  • Tool usage (all time) (usegalaxy.eu): - 1408
  • No. of tool users (5 years) (usegalaxy.org): 32
  • No. - of tool users (all time) (usegalaxy.org): 32
  • Tool usage - (5 years) (usegalaxy.org): 6
  • Tool usage (all time) (usegalaxy.org): - 6
  • No. of tool users (5 years) (usegalaxy.org.au): 6406
  • No. - of tool users (all time) (usegalaxy.org.au): 6406
  • Tool - usage (5 years) (usegalaxy.org.au): 597
  • Tool usage (all - time) (usegalaxy.org.au): 597
  • No. of tool users (5 years) - - all main servers: 15086
  • No. of tool users (all time) - - all main servers: 15086
  • Tool usage (5 years) - all main - servers: 2011
  • Tool usage (all time) - all main servers: - 2011
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Funannotate is a genome prediction, annotation, and comparison + software package. title_md: funannotate - - description_md: '
  • Galaxy tool ids: getmlst
  • Description: - Download MLST datasets by species from pubmlst.org
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: nan
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: getmlst
  • Date - of first commit of the suite: 2015-12-03
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: nan
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst
  • Galaxy - wrapper version: 0.1.4.1
  • Conda id: srst2
  • Conda - version: 0.2.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Download MLST datasets by species from pubmlst.org title_md: getmlst - - description_md: '
  • Galaxy tool ids: ggplot2_heatmap, ggplot2_pca, - ggplot2_histogram, ggplot2_point, ggplot2_violin
  • 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.
  • bio.tool - id: ggplot2
  • bio.tool ids: ggplot2
  • biii: - nan
  • bio.tool name: ggplot2
  • bio.tool description: - Plotting system for R, based on the grammar of graphics.
  • EDAM - operation: Visualisation
  • EDAM topic: Data visualisation
  • Status: - To update
  • Source: https://github.com/tidyverse/ggplot2
  • ToolShed - categories: Visualization
  • ToolShed id: nan
  • Date - of first commit of the suite: 2018-04-26
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2
  • Galaxy - wrapper version: 3.4.0
  • Conda id: r-base
  • Conda - version: nan
  • EDAM operation (no superclasses): Visualisation
  • EDAM - topic (no superclasses): Data visualisation
  • Available on - UseGalaxy.org (Main): 5
  • Available on UseGalaxy.org.au: - 5
  • Available on UseGalaxy.eu: 5
  • Available - on UseGalaxy.fr: 5
  • Tools available on UseGalaxy.org (Main): - 5
  • Tools available on UseGalaxy.org.au: 5
  • Tools - available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: - 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: 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.no: - 5
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 24606
  • No. of tool - users (all time) (usegalaxy.eu): 25662
  • Tool usage (5 years) - (usegalaxy.eu): 3463
  • Tool usage (all time) (usegalaxy.eu): - 3630
  • No. of tool users (5 years) (usegalaxy.org): 26805
  • No. - of tool users (all time) (usegalaxy.org): 26808
  • Tool usage - (5 years) (usegalaxy.org): 5143
  • Tool usage (all time) (usegalaxy.org): - 5144
  • No. of tool users (5 years) (usegalaxy.org.au): 8174
  • No. - of tool users (all time) (usegalaxy.org.au): 8237
  • Tool - usage (5 years) (usegalaxy.org.au): 1259
  • Tool usage (all - time) (usegalaxy.org.au): 1279
  • No. of tool users (5 years) - - all main servers: 59585
  • No. of tool users (all time) - - all main servers: 60707
  • Tool usage (5 years) - all main - servers: 9865
  • Tool usage (all time) - all main servers: - 10053
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: 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. title_md: ggplot2 - - description_md: '
  • Galaxy tool ids: Fetch Taxonomic Ranks
  • Description: - Fetch taxonomic representation
  • bio.tool id: gi2taxonomy
  • bio.tool - ids: gi2taxonomy
  • biii: nan
  • bio.tool - name: gi2taxonomy
  • 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).
  • EDAM - operation: Database search, ID mapping
  • EDAM topic: - Taxonomy
  • Status: To update
  • Source: - https://bitbucket.org/natefoo/taxonomy
  • ToolShed categories: - Metagenomics
  • ToolShed id: gi2taxonomy
  • Date - of first commit of the suite: 2014-01-27
  • Galaxy wrapper - owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy
  • Galaxy - wrapper version: 1.1.1
  • Conda id: taxonomy
  • Conda - version: 0.10.0
  • EDAM operation (no superclasses): - Database search, ID mapping
  • EDAM topic (no superclasses): - Taxonomy
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 490
  • No. of tool - users (all time) (usegalaxy.eu): 682
  • Tool usage (5 years) - (usegalaxy.eu): 74
  • Tool usage (all time) (usegalaxy.eu): - 109
  • No. of tool users (5 years) (usegalaxy.org): 127
  • No. - of tool users (all time) (usegalaxy.org): 14058
  • Tool usage - (5 years) (usegalaxy.org): 20
  • Tool usage (all time) (usegalaxy.org): - 1798
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 617
  • No. - of tool users (all time) - all main servers: 14740
  • Tool - usage (5 years) - all main servers: 94
  • Tool usage (all - time) - all main servers: 1907
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Fetch taxonomic representation title_md: gi2taxonomy - - description_md: '
  • 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
  • Description: - Glimmer makes gene predictions.
  • bio.tool id: gemini
  • bio.tool - ids: gemini
  • biii: nan
  • bio.tool name: - GEMINI
  • 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.
  • EDAM - operation: Sequence analysis, Genetic variation analysis
  • EDAM - topic: Sequence analysis
  • Status: To update
  • Source: - https://ccb.jhu.edu/software/glimmer/
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: nan
  • Date of - first commit of the suite: 2017-11-28
  • Galaxy wrapper owner: - bgruening
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer
  • Galaxy - wrapper version: nan
  • Conda id: glimmer
  • Conda - version: 3.02
  • EDAM operation (no superclasses): - Sequence analysis, Genetic variation analysis
  • EDAM topic (no superclasses): - Sequence analysis
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 4
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 4
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 4343
  • No. of tool - users (all time) (usegalaxy.eu): 4343
  • Tool usage (5 years) - (usegalaxy.eu): 407
  • Tool usage (all time) (usegalaxy.eu): - 407
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 4343
  • No. - of tool users (all time) - all main servers: 4343
  • Tool - usage (5 years) - all main servers: 407
  • Tool usage (all - time) - all main servers: 407
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Glimmer makes gene predictions. title_md: glimmer - - description_md: '
  • Galaxy tool ids: nan
  • Description: - GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: https://ccb.jhu.edu/software/glimmerhmm/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: glimmer_hmm
  • Date - of first commit of the suite: 2015-02-28
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm
  • Galaxy - wrapper version: nan
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: GlimmerHMM is a new gene finder based on a Generalized Hidden + Markov Model (GHMM) title_md: glimmer_hmm - - description_md: "
  • Galaxy tool ids: goenrichment, goslimmer
  • Description:\ - \ Performs GO Enrichment analysis.
  • bio.tool id: goenrichment
  • bio.tool\ - \ ids: goenrichment
  • biii: nan
  • bio.tool\ - \ name: GOEnrichment
  • 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.
  • EDAM\ - \ operation: Gene-set enrichment analysis
  • EDAM topic:\ - \ Transcriptomics
  • Status: Up-to-date
  • Source:\ - \ https://github.com/DanFaria/GOEnrichment
  • ToolShed categories:\ - \ Genome annotation
  • ToolShed id: nan
  • Date\ - \ of first commit of the suite: 2018-12-28
  • Galaxy wrapper\ - \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment
  • Galaxy\ - \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment
  • Galaxy\ - \ wrapper version: 2.0.1
  • Conda id: goenrichment
  • Conda\ - \ version: 2.0.1
  • EDAM operation (no superclasses):\ - \ Gene-set enrichment analysis
  • EDAM topic (no superclasses):\ - \ Transcriptomics
  • Available on UseGalaxy.org (Main): 2
  • Available\ - \ on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu:\ - \ 2
  • Available on UseGalaxy.fr: 2
  • Tools available\ - \ on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au:\ - \ 2
  • Tools available on UseGalaxy.eu: 2
  • Tools\ - \ available on UseGalaxy.fr: 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: 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.no: 2
  • Tools\ - \ available on Viral Variant Visualizer (VVV): 0
  • No. of\ - \ tool users (5 years) (usegalaxy.eu): 5800
  • No. of tool\ - \ users (all time) (usegalaxy.eu): 6212
  • Tool usage (5 years)\ - \ (usegalaxy.eu): 826
  • Tool usage (all time) (usegalaxy.eu):\ - \ 871
  • No. of tool users (5 years) (usegalaxy.org): 7756
  • No.\ - \ of tool users (all time) (usegalaxy.org): 7756
  • Tool usage\ - \ (5 years) (usegalaxy.org): 1048
  • Tool usage (all time)\ - \ (usegalaxy.org): 1048
  • No. of tool users (5 years) (usegalaxy.org.au):\ - \ 1149
  • No. of tool users (all time) (usegalaxy.org.au):\ - \ 1149
  • Tool usage (5 years) (usegalaxy.org.au): 215
  • Tool\ - \ usage (all time) (usegalaxy.org.au): 215
  • No. of tool\ - \ users (5 years) - all main servers: 14705
  • No. of tool\ - \ users (all time) - all main servers: 15117
  • Tool usage\ - \ (5 years) - all main servers: 2089
  • Tool usage (all time)\ - \ - all main servers: 2134
  • Reviewed: True
  • To\ - \ keep: True
  • Deprecated: False
" + - description_md: Performs GO Enrichment analysis. title_md: goenrichment - - description_md: '
  • Galaxy tool ids: goseq
  • Description: - goseq does selection-unbiased testing for category enrichment amongst differentially - expressed (DE) genes for RNA-seq data
  • bio.tool id: goseq
  • bio.tool - ids: goseq
  • biii: nan
  • bio.tool name: - GOseq
  • bio.tool description: Detect Gene Ontology and/or - other user defined categories which are over/under represented in RNA-seq data.
  • EDAM - operation: Gene functional annotation
  • EDAM topic: - RNA-Seq
  • Status: To update
  • Source: - https://bioconductor.org/packages/release/bioc/html/goseq.html
  • ToolShed - categories: Statistics, RNA, Micro-array Analysis
  • ToolShed - id: goseq
  • Date of first commit of the suite: 2018-09-30
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq
  • Galaxy - wrapper version: 1.50.0
  • Conda id: bioconductor-goseq
  • Conda - version: 1.54.0
  • EDAM operation (no superclasses): - Gene functional annotation
  • EDAM topic (no superclasses): - RNA-Seq
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 20207
  • No. of tool - users (all time) (usegalaxy.eu): 21960
  • Tool usage (5 years) - (usegalaxy.eu): 2807
  • Tool usage (all time) (usegalaxy.eu): - 3139
  • No. of tool users (5 years) (usegalaxy.org): 24488
  • No. - of tool users (all time) (usegalaxy.org): 26198
  • Tool usage - (5 years) (usegalaxy.org): 3066
  • Tool usage (all time) (usegalaxy.org): - 3321
  • No. of tool users (5 years) (usegalaxy.org.au): 4155
  • No. - of tool users (all time) (usegalaxy.org.au): 4155
  • Tool - usage (5 years) (usegalaxy.org.au): 545
  • Tool usage (all - time) (usegalaxy.org.au): 545
  • No. of tool users (5 years) - - all main servers: 48850
  • No. of tool users (all time) - - all main servers: 52313
  • Tool usage (5 years) - all main - servers: 6418
  • Tool usage (all time) - all main servers: - 7005
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: goseq does selection-unbiased testing for category enrichment + amongst differentially expressed (DE) genes for RNA-seq data title_md: goseq - - description_md: '
  • Galaxy tool ids: graphlan, graphlan_annotate
  • Description: - GraPhlAn is a software tool for producing high-quality circular representations - of taxonomic and phylogenetic trees
  • bio.tool id: graphlan
  • bio.tool - ids: graphlan
  • biii: nan
  • bio.tool name: - GraPhlAn
  • 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.
  • EDAM - operation: Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic - tree editing, Taxonomic classification
  • EDAM topic: Metagenomics, - Phylogenetics, Phylogenomics, Cladistics
  • Status: To update
  • Source: - https://github.com/biobakery/graphlan
  • ToolShed categories: - Metagenomics, Graphics, Phylogenetics
  • ToolShed id: graphlan
  • Date - of first commit of the suite: 2017-03-03
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan
  • Galaxy - wrapper version: nan
  • Conda id: graphlan
  • Conda - version: 1.1.3
  • EDAM operation (no superclasses): - Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, - Taxonomic classification
  • EDAM topic (no superclasses): - Metagenomics, Phylogenetics, Phylogenomics, Cladistics
  • Available - on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: - 2
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: - 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 9816
  • No. of tool - users (all time) (usegalaxy.eu): 10927
  • Tool usage (5 years) - (usegalaxy.eu): 1285
  • Tool usage (all time) (usegalaxy.eu): - 1350
  • No. of tool users (5 years) (usegalaxy.org): 1273
  • No. - of tool users (all time) (usegalaxy.org): 1273
  • Tool usage - (5 years) (usegalaxy.org): 368
  • Tool usage (all time) (usegalaxy.org): - 368
  • No. of tool users (5 years) (usegalaxy.org.au): 1104
  • No. - of tool users (all time) (usegalaxy.org.au): 1104
  • Tool - usage (5 years) (usegalaxy.org.au): 242
  • Tool usage (all - time) (usegalaxy.org.au): 242
  • No. of tool users (5 years) - - all main servers: 12193
  • No. of tool users (all time) - - all main servers: 13304
  • Tool usage (5 years) - all main - servers: 1895
  • Tool usage (all time) - all main servers: - 1960
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: GraPhlAn is a software tool for producing high-quality circular + representations of taxonomic and phylogenetic trees title_md: graphlan - - description_md: '
  • Galaxy tool ids: graphmap_align, graphmap_overlap
  • Description: - Mapper for long, error-prone reads.
  • bio.tool id: graphmap
  • bio.tool - ids: graphmap
  • biii: nan
  • bio.tool name: - graphmap
  • 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
  • EDAM operation: - Sequence trimming, EST assembly, Read mapping
  • EDAM topic: - Gene transcripts, RNA-Seq, RNA splicing
  • Status: To update
  • Source: - https://github.com/isovic/graphmap/
  • ToolShed categories: - Assembly
  • ToolShed id: graphmap
  • Date of first - commit of the suite: 2018-09-27
  • Galaxy wrapper owner: - bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/graphmap
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/graphmap
  • Galaxy - wrapper version: 0.5.2
  • Conda id: graphmap
  • Conda - version: 0.6.4
  • EDAM operation (no superclasses): - Sequence trimming, EST assembly, Read mapping
  • EDAM topic (no superclasses): - Gene transcripts, RNA-Seq, RNA splicing
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 2
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 2
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 7012
  • No. of tool users (all time) (usegalaxy.eu): 7344
  • Tool - usage (5 years) (usegalaxy.eu): 323
  • Tool usage (all time) - (usegalaxy.eu): 338
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 7012
  • No. of tool users (all time) - all main - servers: 7344
  • Tool usage (5 years) - all main servers: - 323
  • Tool usage (all time) - all main servers: 338
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Mapper for long, error-prone reads. title_md: graphmap - - description_md: '
  • Galaxy tool ids: gtdbtk_classify_wf
  • 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.
  • bio.tool - id: GTDB-Tk
  • bio.tool ids: GTDB-Tk
  • biii: - nan
  • bio.tool name: GTDB-Tk
  • 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).
  • EDAM - operation: Genome alignment, Taxonomic classification, Sequence assembly, - Query and retrieval
  • EDAM topic: Metagenomics, Taxonomy, - Phylogenetics, Database management, Proteins
  • Status: Up-to-date
  • Source: - https://github.com/Ecogenomics/GTDBTk
  • ToolShed categories: - Metagenomics
  • ToolShed id: gtdbtk
  • Date of - first commit of the suite: 2022-12-13
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk
  • Galaxy - wrapper version: 2.4.0
  • Conda id: gtdbtk
  • Conda - version: 2.4.0
  • EDAM operation (no superclasses): - Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval
  • EDAM - topic (no superclasses): Metagenomics, Taxonomy, Phylogenetics, Database - management, Proteins
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 476
  • No. of tool users (all time) (usegalaxy.eu): 476
  • Tool - usage (5 years) (usegalaxy.eu): 87
  • Tool usage (all time) - (usegalaxy.eu): 87
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 588
  • No. of tool users (all time) (usegalaxy.org.au): 588
  • Tool - usage (5 years) (usegalaxy.org.au): 74
  • Tool usage (all - time) (usegalaxy.org.au): 74
  • No. of tool users (5 years) - - all main servers: 1064
  • No. of tool users (all time) - - all main servers: 1064
  • Tool usage (5 years) - all main - servers: 161
  • Tool usage (all time) - all main servers: - 161
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: '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. ' title_md: gtdbtk - - description_md: '
  • Galaxy tool ids: gubbins
  • Description: - Gubbins - bacterial recombination detection
  • bio.tool id: - gubbins
  • bio.tool ids: gubbins
  • biii: - nan
  • bio.tool name: Gubbins
  • bio.tool description: - Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant - bacterial whole genome sequences.
  • EDAM operation: Genotyping, - Phylogenetic inference, Ancestral reconstruction
  • EDAM topic: - Phylogeny, Genotype and phenotype, Whole genome sequencing
  • Status: - To update
  • Source: nan
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: gubbins
  • Date - of first commit of the suite: 2017-06-22
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins
  • Galaxy - wrapper version: 3.2.1
  • Conda id: gubbins
  • Conda - version: 3.3.5
  • EDAM operation (no superclasses): - Genotyping, Phylogenetic inference, Ancestral reconstruction
  • EDAM - topic (no superclasses): Phylogeny, Genotype and phenotype, Whole genome - sequencing
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 3690
  • No. of tool - users (all time) (usegalaxy.eu): 3811
  • Tool usage (5 years) - (usegalaxy.eu): 326
  • Tool usage (all time) (usegalaxy.eu): - 336
  • No. of tool users (5 years) (usegalaxy.org): 3323
  • No. - of tool users (all time) (usegalaxy.org): 3323
  • Tool usage - (5 years) (usegalaxy.org): 235
  • Tool usage (all time) (usegalaxy.org): - 235
  • No. of tool users (5 years) (usegalaxy.org.au): 1895
  • No. - of tool users (all time) (usegalaxy.org.au): 2429
  • Tool - usage (5 years) (usegalaxy.org.au): 234
  • Tool usage (all - time) (usegalaxy.org.au): 258
  • No. of tool users (5 years) - - all main servers: 8908
  • No. of tool users (all time) - - all main servers: 9563
  • Tool usage (5 years) - all main - servers: 795
  • Tool usage (all time) - all main servers: - 829
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Gubbins - bacterial recombination detection title_md: gubbins - - description_md: '
  • Galaxy tool ids: hamronize_summarize, hamronize_tool
  • Description: - Convert AMR gene detection tool output to hAMRonization specification format.
  • bio.tool - id: hamronization
  • bio.tool ids: hamronization
  • biii: - nan
  • bio.tool name: hAMRonization
  • bio.tool - description: Parse multiple Antimicrobial Resistance Analysis Reports - into a common data structure
  • EDAM operation: Data handling, - Antimicrobial resistance prediction, Parsing
  • EDAM topic: - Public health and epidemiology, Microbiology, Bioinformatics
  • Status: - Up-to-date
  • Source: https://github.com/pha4ge/hAMRonization
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: hamronization
  • Date - of first commit of the suite: 2021-02-02
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization
  • Galaxy - wrapper version: 1.1.4
  • Conda id: hamronization
  • Conda - version: 1.1.4
  • EDAM operation (no superclasses): - Antimicrobial resistance prediction, Parsing
  • EDAM topic (no superclasses): - Public health and epidemiology, Microbiology, Bioinformatics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: - 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 7303
  • No. of tool - users (all time) (usegalaxy.eu): 7303
  • Tool usage (5 years) - (usegalaxy.eu): 222
  • Tool usage (all time) (usegalaxy.eu): - 222
  • No. of tool users (5 years) (usegalaxy.org): 20
  • No. - of tool users (all time) (usegalaxy.org): 20
  • Tool usage - (5 years) (usegalaxy.org): 2
  • Tool usage (all time) (usegalaxy.org): - 2
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 7323
  • No. - of tool users (all time) - all main servers: 7323
  • Tool - usage (5 years) - all main servers: 224
  • Tool usage (all - time) - all main servers: 224
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Convert AMR gene detection tool output to hAMRonization specification + format. title_md: hamronization - - description_md: '
  • Galaxy tool ids: bio_hansel
  • Description: - Heidelberg and Enteritidis SNP Elucidation
  • bio.tool id: - Biohansel
  • bio.tool ids: Biohansel
  • biii: - nan
  • bio.tool name: BioHansel
  • 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.
  • EDAM operation: - Genotyping, SNP detection, Genome assembly
  • EDAM topic: - Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious - disease, Agricultural science
  • Status: Up-to-date
  • Source: - https://github.com/phac-nml/bio_hansel
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: bio_hansel
  • Date - of first commit of the suite: 2017-09-29
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel
  • Galaxy - wrapper version: 2.6.1
  • Conda id: bio_hansel
  • Conda - version: 2.6.1
  • EDAM operation (no superclasses): - Genotyping, SNP detection, Genome assembly
  • EDAM topic (no superclasses): - Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious - disease, Agricultural science
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 349
  • No. of tool users (all time) (usegalaxy.eu): 359
  • Tool - usage (5 years) (usegalaxy.eu): 32
  • Tool usage (all time) - (usegalaxy.eu): 33
  • No. of tool users (5 years) (usegalaxy.org): - 364
  • No. of tool users (all time) (usegalaxy.org): 364
  • Tool - usage (5 years) (usegalaxy.org): 53
  • Tool usage (all time) - (usegalaxy.org): 53
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 713
  • No. of tool users (all time) - all main - servers: 723
  • Tool usage (5 years) - all main servers: - 85
  • Tool usage (all time) - all main servers: 86
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Heidelberg and Enteritidis SNP Elucidation title_md: hansel - - description_md: '
  • Galaxy tool ids: hifiasm_meta
  • Description: - A hifiasm fork for metagenome assembly using Hifi reads.
  • bio.tool - id: hifiasm-meta
  • bio.tool ids: hifiasm-meta
  • biii: - nan
  • bio.tool name: Hifiasm-meta
  • bio.tool - description: Hifiasm_meta - de novo metagenome assembler, based on hifiasm, - a haplotype-resolved de novo assembler for PacBio Hifi reads.
  • EDAM - operation: Sequence assembly
  • EDAM topic: Sequence - assembly, Metagenomics
  • Status: To update
  • Source: - https://github.com/xfengnefx/hifiasm-meta
  • ToolShed categories: - Metagenomics
  • ToolShed id: hifiasm_meta
  • Date - of first commit of the suite: 2023-01-18
  • Galaxy wrapper - owner: galaxy-australia
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta
  • Galaxy - wrapper version: 0.3.1
  • Conda id: hifiasm_meta
  • Conda - version: hamtv0.3.1
  • EDAM operation (no superclasses): - Sequence assembly
  • EDAM topic (no superclasses): Sequence - assembly, Metagenomics
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 156
  • No. of tool users (all time) (usegalaxy.eu): 156
  • Tool - usage (5 years) (usegalaxy.eu): 20
  • Tool usage (all time) - (usegalaxy.eu): 20
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 220
  • No. of tool users (all time) (usegalaxy.org.au): 220
  • Tool - usage (5 years) (usegalaxy.org.au): 11
  • Tool usage (all - time) (usegalaxy.org.au): 11
  • No. of tool users (5 years) - - all main servers: 376
  • No. of tool users (all time) - - all main servers: 376
  • Tool usage (5 years) - all main servers: - 31
  • Tool usage (all time) - all main servers: 31
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: A hifiasm fork for metagenome assembly using Hifi reads. title_md: hifiasm_meta - - description_md: '
  • Galaxy tool ids: hivtrace
  • 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.
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - nan
  • ToolShed categories: Sequence Analysis
  • ToolShed - id: hivtrace
  • Date of first commit of the suite: - 2015-12-10
  • Galaxy wrapper owner: nml
  • Galaxy - wrapper source: https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace
  • Galaxy - wrapper version: 1.0.1
  • Conda id: hivtrace
  • Conda - version: 1.5.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: 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. title_md: hivtrace - - description_md: '
  • 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
  • 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).
  • bio.tool - id: hmmer3
  • bio.tool ids: hmmer3
  • biii: - nan
  • bio.tool name: HMMER3
  • 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.
  • 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 topic: Sequence analysis, Sequence - sites, features and motifs, Gene and protein families
  • Status: - Up-to-date
  • Source: http://hmmer.org/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: nan
  • Date - of first commit of the suite: 2016-11-14
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3
  • Galaxy - wrapper version: 3.4
  • Conda id: hmmer
  • Conda - version: 3.4
  • 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 (no superclasses): Sequence analysis, Sequence sites, features - and motifs, Gene and protein families
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 12
  • Available - on UseGalaxy.eu: 12
  • Available on UseGalaxy.fr: 12
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 12
  • Tools available on UseGalaxy.eu: - 12
  • Tools available on UseGalaxy.fr: 12
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 12
  • Tools available on Viral - Variant Visualizer (VVV): 0
  • No. of tool users (5 years) - (usegalaxy.eu): 35919
  • No. of tool users (all time) (usegalaxy.eu): - 36952
  • Tool usage (5 years) (usegalaxy.eu): 1283
  • Tool - usage (all time) (usegalaxy.eu): 1321
  • No. of tool users - (5 years) (usegalaxy.org): 0
  • No. of tool users (all time) - (usegalaxy.org): 0
  • Tool usage (5 years) (usegalaxy.org): - 0
  • Tool usage (all time) (usegalaxy.org): 0
  • No. - of tool users (5 years) (usegalaxy.org.au): 3023
  • No. of - tool users (all time) (usegalaxy.org.au): 3023
  • Tool usage - (5 years) (usegalaxy.org.au): 180
  • Tool usage (all time) - (usegalaxy.org.au): 180
  • No. of tool users (5 years) - all - main servers: 38942
  • No. of tool users (all time) - all - main servers: 39975
  • Tool usage (5 years) - all main servers: - 1463
  • Tool usage (all time) - all main servers: 1501
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: 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). title_md: hmmer3 - - description_md: "
  • 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
  • Description:\ - \ HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level\ - \ resolution
  • bio.tool id: humann
  • bio.tool\ - \ ids: humann
  • biii: nan
  • bio.tool name:\ - \ humann
  • 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
  • EDAM operation: Species\ - \ frequency estimation, Taxonomic classification, Phylogenetic analysis
  • EDAM\ - \ topic: Metagenomics, Phylogenomics
  • Status: Up-to-date
  • Source:\ - \ http://huttenhower.sph.harvard.edu/humann
  • ToolShed categories:\ - \ Metagenomics
  • ToolShed id: humann
  • Date of\ - \ first commit of the suite: 2021-05-12
  • Galaxy wrapper\ - \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann
  • Galaxy\ - \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann
  • Galaxy\ - \ wrapper version: 3.9
  • Conda id: humann
  • Conda\ - \ version: 3.9
  • EDAM operation (no superclasses):\ - \ Species frequency estimation, Taxonomic classification, Phylogenetic analysis
  • EDAM\ - \ topic (no superclasses): Metagenomics, Phylogenomics
  • Available\ - \ on UseGalaxy.org (Main): 6
  • Available on UseGalaxy.org.au:\ - \ 10
  • Available on UseGalaxy.eu: 10
  • Available\ - \ on UseGalaxy.fr: 10
  • Tools available on UseGalaxy.org\ - \ (Main): 6
  • Tools available on UseGalaxy.org.au:\ - \ 10
  • Tools available on UseGalaxy.eu: 10
  • Tools\ - \ available on UseGalaxy.fr: 10
  • Tools available on APOSTL:\ - \ 0
  • Tools available on ARGs-OAP: 0
  • Tools\ - \ available on CIRM-CFBP: 0
  • Tools available on ChemFlow:\ - \ 0
  • Tools available on Coloc-stats: 0
  • Tools\ - \ available on CropGalaxy: 0
  • Tools available 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.no: 10
  • Tools\ - \ available on Viral Variant Visualizer (VVV): 0
  • No. of\ - \ tool users (5 years) (usegalaxy.eu): 26659
  • No. of tool\ - \ users (all time) (usegalaxy.eu): 26659
  • Tool usage (5\ - \ years) (usegalaxy.eu): 2067
  • Tool usage (all time) (usegalaxy.eu):\ - \ 2067
  • No. of tool users (5 years) (usegalaxy.org): 865
  • No.\ - \ of tool users (all time) (usegalaxy.org): 865
  • Tool usage\ - \ (5 years) (usegalaxy.org): 174
  • Tool usage (all time)\ - \ (usegalaxy.org): 174
  • No. of tool users (5 years) (usegalaxy.org.au):\ - \ 3238
  • No. of tool users (all time) (usegalaxy.org.au):\ - \ 3238
  • Tool usage (5 years) (usegalaxy.org.au): 351
  • Tool\ - \ usage (all time) (usegalaxy.org.au): 351
  • No. of tool\ - \ users (5 years) - all main servers: 30762
  • No. of tool\ - \ users (all time) - all main servers: 30762
  • Tool usage\ - \ (5 years) - all main servers: 2592
  • Tool usage (all time)\ - \ - all main servers: 2592
  • Reviewed: True
  • To\ - \ keep: True
  • Deprecated: False
" + - description_md: HUMAnN for functionally profiling metagenomes and metatranscriptomes + at species-level resolution title_md: humann - - description_md: '
  • 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
  • Description: Hypothesis Testing using Phylogenies
  • bio.tool - id: HyPhy
  • bio.tool ids: HyPhy
  • biii: - nan
  • bio.tool name: HyPhy
  • bio.tool description: - Software package for the analysis of genetic sequences using techniques in phylogenetics, - molecular evolution, and machine learning.
  • EDAM operation: - Statistical calculation
  • EDAM topic: Phylogeny, Small molecules, - Molecular interactions, pathways and networks
  • Status: To - update
  • Source: http://www.hyphy.org
  • ToolShed - categories: Phylogenetics
  • ToolShed id: nan
  • Date - of first commit of the suite: 2021-04-19
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy
  • Galaxy - wrapper version: 2.5.47
  • Conda id: hyphy
  • Conda - version: 2.5.62
  • EDAM operation (no superclasses): - Statistical calculation
  • EDAM topic (no superclasses): Phylogeny, - Small molecules, Molecular interactions, pathways and networks
  • Available - on UseGalaxy.org (Main): 17
  • Available on UseGalaxy.org.au: - 2
  • Available on UseGalaxy.eu: 17
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 17
  • Tools available on UseGalaxy.org.au: 2
  • Tools - available on UseGalaxy.eu: 17
  • Tools available on UseGalaxy.fr: - 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 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.no: - 12
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 11429
  • No. of tool - users (all time) (usegalaxy.eu): 11429
  • Tool usage (5 years) - (usegalaxy.eu): 428
  • Tool usage (all time) (usegalaxy.eu): - 428
  • No. of tool users (5 years) (usegalaxy.org): 7751
  • No. - of tool users (all time) (usegalaxy.org): 7751
  • Tool usage - (5 years) (usegalaxy.org): 676
  • Tool usage (all time) (usegalaxy.org): - 676
  • No. of tool users (5 years) (usegalaxy.org.au): 715
  • No. - of tool users (all time) (usegalaxy.org.au): 715
  • Tool usage - (5 years) (usegalaxy.org.au): 58
  • Tool usage (all time) - (usegalaxy.org.au): 58
  • No. of tool users (5 years) - all - main servers: 19895
  • No. of tool users (all time) - all - main servers: 19895
  • Tool usage (5 years) - all main servers: - 1162
  • Tool usage (all time) - all main servers: 1162
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Hypothesis Testing using Phylogenies title_md: hyphy - - description_md: '
  • Galaxy tool ids: hypo
  • Description: - Super Fast & Accurate Polisher for Long Read Genome Assemblies
  • bio.tool - id: HyPo
  • bio.tool ids: HyPo
  • biii: - nan
  • bio.tool name: HyPo
  • 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.
  • EDAM - operation: Optimisation and refinement, Genome assembly
  • EDAM - topic: Sequence assembly, Genomics
  • Status: Up-to-date
  • Source: - https://github.com/kensung-lab/hypo
  • ToolShed categories: - Assembly
  • ToolShed id: hypo
  • Date of first - commit of the suite: 2021-11-15
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo
  • Galaxy - wrapper version: 1.0.3
  • Conda id: hypo
  • Conda - version: 1.0.3
  • EDAM operation (no superclasses): - Optimisation and refinement, Genome assembly
  • EDAM topic (no superclasses): - Sequence assembly, Genomics
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 473
  • No. of tool users (all time) (usegalaxy.eu): 473
  • Tool - usage (5 years) (usegalaxy.eu): 93
  • Tool usage (all time) - (usegalaxy.eu): 93
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 473
  • No. of tool users (all time) - all main - servers: 473
  • Tool usage (5 years) - all main servers: - 93
  • Tool usage (all time) - all main servers: 93
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Super Fast & Accurate Polisher for Long Read Genome Assemblies title_md: hypo - - description_md: '
  • Galaxy tool ids: icescreen
  • Description: - ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative - Mobilizable Elements (IMEs) in Bacillota genomes.
  • bio.tool id: - icescreen
  • bio.tool ids: icescreen
  • biii: - nan
  • bio.tool name: ICEscreen
  • bio.tool description: - A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite - structures.
  • EDAM operation: Database search, Protein feature - detection
  • EDAM topic: Mobile genetic elements, Sequence - sites, features and motifs, Genomics, Molecular interactions, pathways and networks, - Structural variation
  • Status: To update
  • Source: - https://icescreen.migale.inrae.fr/
  • ToolShed categories: - Genome annotation
  • ToolShed id: icescreen
  • Date - of first commit of the suite: 2022-01-04
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://forgemia.inra.fr/ices_imes_analysis/icescreen
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen
  • Galaxy - wrapper version: 1.3.1
  • Conda id: icescreen
  • Conda - version: 1.3.2
  • EDAM operation (no superclasses): - Database search, Protein feature detection
  • EDAM topic (no superclasses): - Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular - interactions, pathways and networks, Structural variation
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: ICEscreen identifies Integrative Conjugative Elements (ICEs) and + Integrative Mobilizable Elements (IMEs) in Bacillota genomes. title_md: icescreen - - description_md: '
  • Galaxy tool ids: idba_hybrid, idba_tran, - idba_ud
  • Description: Wrappers for the idba assembler variants.
  • bio.tool - id: idba
  • bio.tool ids: idba
  • biii: - nan
  • bio.tool name: IDBA
  • 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.
  • EDAM - operation: Sequence assembly
  • EDAM topic: Sequence - assembly
  • Status: To update
  • Source: - https://i.cs.hku.hk/~alse/hkubrg/projects/index.html
  • ToolShed - categories: Assembly
  • ToolShed id: idba
  • Date - of first commit of the suite: 2018-04-26
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud
  • Galaxy - wrapper version: nan
  • Conda id: idba
  • Conda - version: 1.1.3
  • EDAM operation (no superclasses): - Sequence assembly
  • EDAM topic (no superclasses): Sequence - assembly
  • Available on UseGalaxy.org (Main): 3
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 3
  • Available on UseGalaxy.fr: 3
  • Tools available - on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 3
  • Tools - available on UseGalaxy.fr: 3
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools 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.no: - 3
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1200
  • No. of tool - users (all time) (usegalaxy.eu): 1220
  • Tool usage (5 years) - (usegalaxy.eu): 187
  • Tool usage (all time) (usegalaxy.eu): - 195
  • No. of tool users (5 years) (usegalaxy.org): 1588
  • No. - of tool users (all time) (usegalaxy.org): 1588
  • Tool usage - (5 years) (usegalaxy.org): 267
  • Tool usage (all time) (usegalaxy.org): - 267
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 2788
  • No. - of tool users (all time) - all main servers: 2808
  • Tool - usage (5 years) - all main servers: 454
  • Tool usage (all - time) - all main servers: 462
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Wrappers for the idba assembler variants. title_md: idba_ud - - description_md: '
  • Galaxy tool ids: infernal_cmalign, infernal_cmbuild, - infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat
  • Description: - Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases - for RNA structure and sequence similarities.
  • bio.tool id: - infernal
  • bio.tool ids: infernal
  • biii: - nan
  • bio.tool name: Infernal
  • 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.
  • EDAM operation: Nucleic acid feature - detection
  • EDAM topic: Sequence sites, features and motifs, - Structural genomics
  • Status: To update
  • Source: - http://infernal.janelia.org/
  • ToolShed categories: RNA
  • ToolShed - id: infernal
  • Date of first commit of the suite: - 2015-05-07
  • Galaxy wrapper owner: bgruening
  • Galaxy - wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/infernal
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal
  • Galaxy - wrapper version: 1.1.4
  • Conda id: infernal
  • Conda - version: 1.1.5
  • EDAM operation (no superclasses): - Nucleic acid feature detection
  • EDAM topic (no superclasses): - Sequence sites, features and motifs, Structural genomics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 6
  • Available on UseGalaxy.eu: 6
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 6
  • Tools - available on UseGalaxy.eu: 6
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 6
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 59700
  • No. of tool - users (all time) (usegalaxy.eu): 112582
  • Tool usage (5 years) - (usegalaxy.eu): 223
  • Tool usage (all time) (usegalaxy.eu): - 282
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 1157
  • No. - of tool users (all time) (usegalaxy.org.au): 1221
  • Tool - usage (5 years) (usegalaxy.org.au): 34
  • Tool usage (all - time) (usegalaxy.org.au): 35
  • No. of tool users (5 years) - - all main servers: 60857
  • No. of tool users (all time) - - all main servers: 113803
  • Tool usage (5 years) - all main - servers: 257
  • Tool usage (all time) - all main servers: - 317
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence + databases for RNA structure and sequence similarities. title_md: infernal - - description_md: '
  • Galaxy tool ids: instrain_compare, instrain_profile
  • Description: - InStrain is a tool for analysis of co-occurring genome populations from metagenomes
  • bio.tool - id: instrain
  • bio.tool ids: instrain
  • biii: - nan
  • bio.tool name: InStrain
  • 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
  • EDAM operation: SNP detection, - Genome comparison
  • EDAM topic: Mapping, Metagenomics
  • Status: - To update
  • Source: https://instrain.readthedocs.io/en/latest/#
  • ToolShed - categories: Metagenomics
  • ToolShed id: instrain
  • Date - of first commit of the suite: 2021-08-11
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain
  • Galaxy - wrapper version: 1.5.3
  • Conda id: instrain
  • Conda - version: 1.9.0
  • EDAM operation (no superclasses): - SNP detection, Genome comparison
  • EDAM topic (no superclasses): - Mapping, Metagenomics
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 2
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 102
  • No. of tool users (all time) (usegalaxy.eu): 102
  • Tool - usage (5 years) (usegalaxy.eu): 16
  • Tool usage (all time) - (usegalaxy.eu): 16
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 102
  • No. of tool users (all time) - all main - servers: 102
  • Tool usage (5 years) - all main servers: - 16
  • Tool usage (all time) - all main servers: 16
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: InStrain is a tool for analysis of co-occurring genome populations + from metagenomes title_md: instrain - - description_md: '
  • Galaxy tool ids: integron_finder
  • 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"
  • bio.tool - id: integron_finder
  • bio.tool ids: integron_finder
  • biii: - nan
  • bio.tool name: Integron Finder
  • bio.tool - description: A tool to detect Integron in DNA sequences.
  • EDAM - operation: Nucleic acid feature detection, Sequence motif recognition, - Protein feature detection, Genome annotation
  • EDAM topic: - Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis
  • Status: - Up-to-date
  • Source: https://github.com/gem-pasteur/Integron_Finder
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: integronfinder
  • Date - of first commit of the suite: 2022-09-22
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder
  • Galaxy - wrapper version: 2.0.5
  • Conda id: integron_finder
  • Conda - version: 2.0.5
  • EDAM operation (no superclasses): - Nucleic acid feature detection, Sequence motif recognition, Protein feature - detection, Genome annotation
  • EDAM topic (no superclasses): - Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 55149
  • No. of tool - users (all time) (usegalaxy.eu): 55149
  • Tool usage (5 years) - (usegalaxy.eu): 161
  • Tool usage (all time) (usegalaxy.eu): - 161
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 6085
  • No. - of tool users (all time) (usegalaxy.org.au): 6085
  • Tool - usage (5 years) (usegalaxy.org.au): 73
  • Tool usage (all - time) (usegalaxy.org.au): 73
  • No. of tool users (5 years) - - all main servers: 61234
  • No. of tool users (all time) - - all main servers: 61234
  • Tool usage (5 years) - all main - servers: 234
  • Tool usage (all time) - all main servers: - 234
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: '"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"' title_md: integron_finder - - description_md: '
  • Galaxy tool ids: interproscan
  • Description: - Interproscan queries the interpro database and provides annotations.
  • bio.tool - id: interproscan_ebi
  • bio.tool ids: interproscan_ebi
  • biii: - nan
  • bio.tool name: InterProScan (EBI)
  • bio.tool - description: Scan sequences against the InterPro protein signature databases.
  • EDAM - operation: Sequence motif recognition, Protein feature detection
  • EDAM - topic: Gene and protein families, Sequence analysis
  • Status: - To update
  • Source: http://www.ebi.ac.uk/Tools/pfa/iprscan5/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: interproscan
  • Date - of first commit of the suite: 2021-11-15
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan
  • Galaxy - wrapper version: 5.59-91.0
  • Conda id: interproscan
  • Conda - version: 5.59_91.0
  • EDAM operation (no superclasses): - Sequence motif recognition, Protein feature detection
  • EDAM topic - (no superclasses): Gene and protein families, Sequence analysis
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 34689
  • No. of tool - users (all time) (usegalaxy.eu): 55189
  • Tool usage (5 years) - (usegalaxy.eu): 1634
  • Tool usage (all time) (usegalaxy.eu): - 1713
  • No. of tool users (5 years) (usegalaxy.org): 65
  • No. - of tool users (all time) (usegalaxy.org): 65
  • Tool usage - (5 years) (usegalaxy.org): 15
  • Tool usage (all time) (usegalaxy.org): - 15
  • No. of tool users (5 years) (usegalaxy.org.au): 10897
  • No. - of tool users (all time) (usegalaxy.org.au): 10897
  • Tool - usage (5 years) (usegalaxy.org.au): 607
  • Tool usage (all - time) (usegalaxy.org.au): 607
  • No. of tool users (5 years) - - all main servers: 45651
  • No. of tool users (all time) - - all main servers: 66151
  • Tool usage (5 years) - all main - servers: 2256
  • Tool usage (all time) - all main servers: - 2335
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Interproscan queries the interpro database and provides annotations. title_md: interproscan - - description_md: '
  • Galaxy tool ids: nan
  • Description: - Interproscan queries the interpro database and provides annotations.
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: http://www.ebi.ac.uk/Tools/pfa/iprscan5/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: iprscan5
  • Date - of first commit of the suite: 2015-02-28
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5
  • Galaxy - wrapper version: nan
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Interproscan queries the interpro database and provides annotations. title_md: iprscan5 - - description_md: '
  • Galaxy tool ids: iqtree
  • Description: - Efficient phylogenomic software by maximum likelihood
  • bio.tool - id: iqtree
  • bio.tool ids: iqtree
  • biii: - nan
  • bio.tool name: iqtree
  • 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
  • EDAM operation: Phylogenetic - analysis, Sequence analysis
  • EDAM topic: Phylogenetics
  • Status: - Up-to-date
  • Source: http://www.iqtree.org/
  • ToolShed - categories: Phylogenetics
  • ToolShed id: iqtree
  • Date - of first commit of the suite: 2017-11-15
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree
  • Galaxy - wrapper version: 2.3.6
  • Conda id: iqtree
  • Conda - version: 2.3.6
  • EDAM operation (no superclasses): - Phylogenetic analysis, Sequence analysis
  • EDAM topic (no superclasses): - Phylogenetics
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 28279
  • No. of tool - users (all time) (usegalaxy.eu): 28481
  • Tool usage (5 years) - (usegalaxy.eu): 1623
  • Tool usage (all time) (usegalaxy.eu): - 1646
  • No. of tool users (5 years) (usegalaxy.org): 24662
  • No. - of tool users (all time) (usegalaxy.org): 24662
  • Tool usage - (5 years) (usegalaxy.org): 2093
  • Tool usage (all time) (usegalaxy.org): - 2093
  • No. of tool users (5 years) (usegalaxy.org.au): 9780
  • No. - of tool users (all time) (usegalaxy.org.au): 10086
  • Tool - usage (5 years) (usegalaxy.org.au): 979
  • Tool usage (all - time) (usegalaxy.org.au): 992
  • No. of tool users (5 years) - - all main servers: 62721
  • No. of tool users (all time) - - all main servers: 63229
  • Tool usage (5 years) - all main - servers: 4695
  • Tool usage (all time) - all main servers: - 4731
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Efficient phylogenomic software by maximum likelihood title_md: iqtree - - description_md: '
  • Galaxy tool ids: isescan
  • 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."
  • bio.tool id: ISEScan
  • bio.tool - ids: ISEScan
  • biii: nan
  • bio.tool name: - ISEScan
  • bio.tool description: Automated identification - of insertion sequence elements in prokaryotic genomes.
  • EDAM operation: - Structural variation detection
  • EDAM topic: Genomics, DNA - structural variation, Sequence analysis, Genetic variation
  • Status: - To update
  • Source: https://github.com/xiezhq/ISEScan
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: ISEScan
  • Date - of first commit of the suite: 2022-09-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan
  • Galaxy - wrapper version: 1.7.2.3
  • Conda id: isescan
  • Conda - version: 1.7.2.1
  • EDAM operation (no superclasses): - Structural variation detection
  • EDAM topic (no superclasses): - Genomics, Sequence analysis, Genetic variation
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 59386
  • No. of tool users (all time) (usegalaxy.eu): 59386
  • Tool - usage (5 years) (usegalaxy.eu): 151
  • Tool usage (all time) - (usegalaxy.eu): 151
  • No. of tool users (5 years) (usegalaxy.org): - 56
  • No. of tool users (all time) (usegalaxy.org): 56
  • Tool - usage (5 years) (usegalaxy.org): 1
  • Tool usage (all time) - (usegalaxy.org): 1
  • No. of tool users (5 years) (usegalaxy.org.au): - 4741
  • No. of tool users (all time) (usegalaxy.org.au): 4741
  • Tool - usage (5 years) (usegalaxy.org.au): 59
  • Tool usage (all - time) (usegalaxy.org.au): 59
  • No. of tool users (5 years) - - all main servers: 64183
  • No. of tool users (all time) - - all main servers: 64183
  • Tool usage (5 years) - all main - servers: 211
  • Tool usage (all time) - all main servers: - 211
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: '"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."' title_md: isescan - - description_md: '
  • Galaxy tool ids: itsx
  • Description: - ITSx is an open source software utility to extract the highly variable ITS1 - and ITS2 subregions from ITS sequences.
  • bio.tool id: ITSx
  • bio.tool - ids: ITSx
  • biii: nan
  • bio.tool name: - ITSx
  • 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.
  • EDAM - operation: Sequence feature detection
  • EDAM topic: - Functional, regulatory and non-coding RNA, Microbiology
  • Status: - Up-to-date
  • Source: https://microbiology.se/software/itsx/
  • ToolShed - categories: Metagenomics
  • ToolShed id: itsx
  • Date - of first commit of the suite: 2022-05-02
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/itsx
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/itsx
  • Galaxy - wrapper version: 1.1.3
  • Conda id: itsx
  • Conda - version: 1.1.3
  • EDAM operation (no superclasses): - Sequence feature detection
  • EDAM topic (no superclasses): - Functional, regulatory and non-coding RNA, Microbiology
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1426
  • No. of tool - users (all time) (usegalaxy.eu): 1426
  • Tool usage (5 years) - (usegalaxy.eu): 71
  • Tool usage (all time) (usegalaxy.eu): - 71
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1426
  • No. - of tool users (all time) - all main servers: 1426
  • Tool - usage (5 years) - all main servers: 71
  • Tool usage (all - time) - all main servers: 71
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: ITSx is an open source software utility to extract the highly + variable ITS1 and ITS2 subregions from ITS sequences. title_md: itsx - - description_md: '
  • Galaxy tool ids: ivar_consensus, ivar_filtervariants, - ivar_removereads, ivar_trim, ivar_variants
  • Description: - iVar is a computational package that contains functions broadly useful for viral - amplicon-based sequencing
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: - https://github.com/andersen-lab/ivar
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: ivar
  • Date - of first commit of the suite: 2020-06-05
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar
  • Galaxy - wrapper version: 1.4.3
  • Conda id: ivar
  • Conda - version: 1.4.3
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 5
  • Available on UseGalaxy.org.au: - 5
  • Available on UseGalaxy.eu: 5
  • Available - on UseGalaxy.fr: 5
  • Tools available on UseGalaxy.org (Main): - 5
  • Tools available on UseGalaxy.org.au: 5
  • Tools - available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: - 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: - 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.no: - 5
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1252220
  • No. of - tool users (all time) (usegalaxy.eu): 1252220
  • Tool usage - (5 years) (usegalaxy.eu): 2366
  • Tool usage (all time) (usegalaxy.eu): - 2366
  • No. of tool users (5 years) (usegalaxy.org): 126027
  • No. - of tool users (all time) (usegalaxy.org): 126027
  • Tool usage - (5 years) (usegalaxy.org): 2496
  • Tool usage (all time) (usegalaxy.org): - 2496
  • No. of tool users (5 years) (usegalaxy.org.au): 41901
  • No. - of tool users (all time) (usegalaxy.org.au): 41901
  • Tool - usage (5 years) (usegalaxy.org.au): 993
  • Tool usage (all - time) (usegalaxy.org.au): 993
  • No. of tool users (5 years) - - all main servers: 1420148
  • No. of tool users (all time) - - all main servers: 1420148
  • Tool usage (5 years) - all - main servers: 5855
  • Tool usage (all time) - all main servers: - 5855
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: iVar is a computational package that contains functions broadly + useful for viral amplicon-based sequencing title_md: ivar - - description_md: '
  • Galaxy tool ids: jbrowse_to_standalone, - jbrowse
  • Description: JBrowse Genome Browser integrated - as a Galaxy Tool
  • bio.tool id: jbrowse
  • bio.tool - ids: jbrowse
  • biii: nan
  • bio.tool name: - JBrowse
  • 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.
  • EDAM - operation: Genome visualisation
  • EDAM topic: Genomics
  • Status: - Up-to-date
  • Source: https://jbrowse.org
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: jbrowse
  • Date - of first commit of the suite: 2019-08-29
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse
  • Galaxy - wrapper version: 1.16.11
  • Conda id: jbrowse
  • Conda - version: 1.16.11
  • EDAM operation (no superclasses): - Genome visualisation
  • EDAM topic (no superclasses): Genomics
  • Available - on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: - 2
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 21153
  • No. of tool - users (all time) (usegalaxy.eu): 22174
  • Tool usage (5 years) - (usegalaxy.eu): 5514
  • Tool usage (all time) (usegalaxy.eu): - 5779
  • No. of tool users (5 years) (usegalaxy.org): 17428
  • No. - of tool users (all time) (usegalaxy.org): 17428
  • Tool usage - (5 years) (usegalaxy.org): 6458
  • Tool usage (all time) (usegalaxy.org): - 6458
  • No. of tool users (5 years) (usegalaxy.org.au): 15673
  • No. - of tool users (all time) (usegalaxy.org.au): 17267
  • Tool - usage (5 years) (usegalaxy.org.au): 3248
  • Tool usage (all - time) (usegalaxy.org.au): 3786
  • No. of tool users (5 years) - - all main servers: 54254
  • No. of tool users (all time) - - all main servers: 56869
  • Tool usage (5 years) - all main - servers: 15220
  • Tool usage (all time) - all main servers: - 16023
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: JBrowse Genome Browser integrated as a Galaxy Tool title_md: jbrowse - - description_md: '
  • Galaxy tool ids: jellyfish
  • Description: - Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA
  • bio.tool - id: Jellyfish
  • bio.tool ids: Jellyfish
  • biii: - nan
  • bio.tool name: Jellyfish
  • bio.tool description: - A command-line algorithm for counting k-mers in DNA sequence.
  • EDAM - operation: k-mer counting
  • EDAM topic: Sequence analysis, - Genomics
  • Status: To update
  • Source: - https://github.com/gmarcais/Jellyfish
  • ToolShed categories: - Assembly
  • ToolShed id: jellyfish
  • Date of first - commit of the suite: 2021-04-07
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish
  • Galaxy - wrapper version: nan
  • Conda id: kmer-jellyfish
  • Conda - version: 2.3.1
  • EDAM operation (no superclasses): - k-mer counting
  • EDAM topic (no superclasses): Sequence analysis, - Genomics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1825
  • No. of tool - users (all time) (usegalaxy.eu): 1825
  • Tool usage (5 years) - (usegalaxy.eu): 237
  • Tool usage (all time) (usegalaxy.eu): - 237
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 971
  • No. - of tool users (all time) (usegalaxy.org.au): 971
  • Tool usage - (5 years) (usegalaxy.org.au): 56
  • Tool usage (all time) - (usegalaxy.org.au): 56
  • No. of tool users (5 years) - all - main servers: 2796
  • No. of tool users (all time) - all main - servers: 2796
  • Tool usage (5 years) - all main servers: - 293
  • Tool usage (all time) - all main servers: 293
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Jellyfish is a tool for fast, memory-efficient counting of k-mers + in DNA title_md: jellyfish - - description_md: '
  • Galaxy tool ids: kat_@EXECUTABLE@
  • Description: - Filtering kmers or reads from a database of kmers hashes
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: nan
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: kat_filter
  • Date - of first commit of the suite: 2017-03-13
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: nan
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter
  • Galaxy - wrapper version: 2.3
  • Conda id: kat
  • Conda - version: 2.4.2
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Filtering kmers or reads from a database of kmers hashes title_md: kat_filter - - description_md: '
  • Galaxy tool ids: kc-align
  • Description: - Kc-Align custom tool
  • bio.tool id: kc-align
  • bio.tool - ids: kc-align
  • biii: nan
  • bio.tool name: - kc-align
  • bio.tool description: A fast and accurate tool - for performing codon-aware multiple sequence alignments
  • EDAM operation: - Multiple sequence alignment
  • EDAM topic: Mapping
  • Status: - Up-to-date
  • Source: https://github.com/davebx/kc-align
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: kc_align
  • Date - of first commit of the suite: 2020-02-20
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align
  • Galaxy - wrapper version: 1.0.2
  • Conda id: kcalign
  • Conda - version: 1.0.2
  • EDAM operation (no superclasses): - Multiple sequence alignment
  • EDAM topic (no superclasses): - Mapping
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 379
  • No. of tool - users (all time) (usegalaxy.eu): 379
  • Tool usage (5 years) - (usegalaxy.eu): 53
  • Tool usage (all time) (usegalaxy.eu): - 53
  • No. of tool users (5 years) (usegalaxy.org): 8259
  • No. - of tool users (all time) (usegalaxy.org): 8259
  • Tool usage - (5 years) (usegalaxy.org): 271
  • Tool usage (all time) (usegalaxy.org): - 271
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 8638
  • No. - of tool users (all time) - all main servers: 8638
  • Tool - usage (5 years) - all main servers: 324
  • Tool usage (all - time) - all main servers: 324
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Kc-Align custom tool title_md: kc-align - - description_md: '
  • 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
  • Description: - In-memory nucleotide sequence k-mer counting, filtering, graph traversal and - more
  • bio.tool id: khmer
  • bio.tool ids: - khmer
  • biii: nan
  • bio.tool name: khmer
  • 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.
  • EDAM operation: - Standardisation and normalisation, De-novo assembly
  • EDAM topic: - Sequence assembly
  • Status: Up-to-date
  • Source: - https://khmer.readthedocs.org/
  • ToolShed categories: Assembly, - Next Gen Mappers
  • ToolShed id: khmer
  • Date - of first commit of the suite: 2015-11-08
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer
  • Galaxy - wrapper version: 3.0.0a3
  • Conda id: khmer
  • Conda - version: 3.0.0a3
  • EDAM operation (no superclasses): - Standardisation and normalisation, De-novo assembly
  • EDAM topic - (no superclasses): Sequence assembly
  • Available on UseGalaxy.org - (Main): 8
  • Available on UseGalaxy.org.au: 8
  • Available - on UseGalaxy.eu: 8
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 8
  • Tools available on - UseGalaxy.org.au: 8
  • Tools available on UseGalaxy.eu: - 8
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available 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.no: 8
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1995
  • No. of tool users (all time) (usegalaxy.eu): 2091
  • Tool - usage (5 years) (usegalaxy.eu): 174
  • Tool usage (all time) - (usegalaxy.eu): 193
  • No. of tool users (5 years) (usegalaxy.org): - 1430
  • No. of tool users (all time) (usegalaxy.org): 1430
  • Tool - usage (5 years) (usegalaxy.org): 389
  • Tool usage (all time) - (usegalaxy.org): 389
  • No. of tool users (5 years) (usegalaxy.org.au): - 1580
  • No. of tool users (all time) (usegalaxy.org.au): 1580
  • Tool - usage (5 years) (usegalaxy.org.au): 56
  • Tool usage (all - time) (usegalaxy.org.au): 56
  • No. of tool users (5 years) - - all main servers: 5005
  • No. of tool users (all time) - - all main servers: 5101
  • Tool usage (5 years) - all main - servers: 619
  • Tool usage (all time) - all main servers: - 638
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: In-memory nucleotide sequence k-mer counting, filtering, graph + traversal and more title_md: khmer - - description_md: '
  • Galaxy tool ids: kleborate
  • Description: - Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae - species complex (KpSC)
  • bio.tool id: kleborate
  • bio.tool - ids: kleborate
  • biii: nan
  • bio.tool - name: Kleborate
  • 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).
  • EDAM - operation: Multilocus sequence typing, Genome assembly, Virulence prediction
  • EDAM - topic: Public health and epidemiology, Metagenomics, Population genomics, - Sequence assembly, Whole genome sequencing
  • Status: To update
  • Source: - https://github.com/katholt/Kleborate/wiki
  • ToolShed categories: - Metagenomics
  • ToolShed id: kleborate
  • Date - of first commit of the suite: 2022-09-09
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/katholt/Kleborate
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate
  • Galaxy - wrapper version: 2.3.2
  • Conda id: kleborate
  • Conda - version: 3.1.0
  • EDAM operation (no superclasses): - Multilocus sequence typing, Genome assembly, Virulence prediction
  • EDAM - topic (no superclasses): Public health and epidemiology, Metagenomics, - Population genomics, Sequence assembly, Whole genome sequencing
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 503
  • No. of tool - users (all time) (usegalaxy.eu): 503
  • Tool usage (5 years) - (usegalaxy.eu): 58
  • Tool usage (all time) (usegalaxy.eu): - 58
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 503
  • No. - of tool users (all time) - all main servers: 503
  • Tool usage - (5 years) - all main servers: 58
  • Tool usage (all time) - - all main servers: 58
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella + pneumoniae species complex (KpSC) title_md: kleborate - - description_md: '
  • Galaxy tool ids: kofamscan
  • Description: - Gene function annotation tool based on KEGG Orthology and hidden Markov model
  • bio.tool - id: kofamscan
  • bio.tool ids: kofamscan
  • biii: - nan
  • bio.tool name: kofamscan
  • 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.
  • EDAM operation: - Sequence analysis, Gene functional annotation
  • EDAM topic: - Genomics
  • Status: Up-to-date
  • Source: - https://github.com/takaram/kofam_scan
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: kofamscan
  • Date - of first commit of the suite: 2020-11-12
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan
  • Galaxy - wrapper version: 1.3.0
  • Conda id: kofamscan
  • Conda - version: 1.3.0
  • EDAM operation (no superclasses): - Sequence analysis, Gene functional annotation
  • EDAM topic (no superclasses): - Genomics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1342
  • No. of tool - users (all time) (usegalaxy.eu): 1342
  • Tool usage (5 years) - (usegalaxy.eu): 63
  • Tool usage (all time) (usegalaxy.eu): - 63
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1342
  • No. - of tool users (all time) - all main servers: 1342
  • Tool - usage (5 years) - all main servers: 63
  • Tool usage (all - time) - all main servers: 63
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Gene function annotation tool based on KEGG Orthology and hidden + Markov model title_md: kofamscan - - description_md: '
  • Galaxy tool ids: kraken-filter, kraken-mpa-report, - kraken-report, kraken-translate, kraken
  • 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.
  • bio.tool id: kraken
  • bio.tool ids: - kraken
  • biii: nan
  • bio.tool name: Kraken
  • 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.
  • EDAM operation: Taxonomic - classification
  • EDAM topic: Taxonomy, Metagenomics
  • Status: - To update
  • Source: http://ccb.jhu.edu/software/kraken/
  • ToolShed - categories: Metagenomics
  • ToolShed id: kraken
  • Date - of first commit of the suite: 2017-01-24
  • Galaxy wrapper - owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken
  • Galaxy - wrapper version: nan
  • Conda id: kraken
  • Conda - version: 1.1.1
  • EDAM operation (no superclasses): - Taxonomic classification
  • EDAM topic (no superclasses): - Taxonomy, Metagenomics
  • Available on UseGalaxy.org (Main): - 5
  • Available on UseGalaxy.org.au: 5
  • Available - on UseGalaxy.eu: 5
  • Available on UseGalaxy.fr: 5
  • Tools - available on UseGalaxy.org (Main): 5
  • Tools available on - UseGalaxy.org.au: 5
  • Tools available on UseGalaxy.eu: - 5
  • Tools available on UseGalaxy.fr: 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: 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.no: 5
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 48136
  • No. of tool users (all time) (usegalaxy.eu): 48164
  • Tool - usage (5 years) (usegalaxy.eu): 2754
  • Tool usage (all time) - (usegalaxy.eu): 2760
  • No. of tool users (5 years) (usegalaxy.org): - 59952
  • No. of tool users (all time) (usegalaxy.org): 130398
  • Tool - usage (5 years) (usegalaxy.org): 5869
  • Tool usage (all time) - (usegalaxy.org): 8654
  • No. of tool users (5 years) (usegalaxy.org.au): - 29008
  • No. of tool users (all time) (usegalaxy.org.au): - 31148
  • Tool usage (5 years) (usegalaxy.org.au): 1936
  • Tool - usage (all time) (usegalaxy.org.au): 2200
  • No. of tool users - (5 years) - all main servers: 137096
  • No. of tool users - (all time) - all main servers: 209710
  • Tool usage (5 years) - - all main servers: 10559
  • Tool usage (all time) - all main - servers: 13614
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: 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. title_md: kraken - - description_md: '
  • Galaxy tool ids: kraken2
  • Description: - Kraken2 for taxonomic designation.
  • bio.tool id: kraken2
  • bio.tool - ids: kraken2
  • biii: nan
  • bio.tool name: - kraken2
  • 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.
  • EDAM - operation: Taxonomic classification
  • EDAM topic: - Taxonomy, Metagenomics
  • Status: Up-to-date
  • Source: - http://ccb.jhu.edu/software/kraken/
  • ToolShed categories: - Metagenomics
  • ToolShed id: kraken2
  • Date of - first commit of the suite: 2019-03-06
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2
  • Galaxy - wrapper version: 2.1.3
  • Conda id: kraken2
  • Conda - version: 2.1.3
  • EDAM operation (no superclasses): - Taxonomic classification
  • EDAM topic (no superclasses): - Taxonomy, Metagenomics
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 271367
  • No. of tool users (all time) (usegalaxy.eu): 271786
  • Tool - usage (5 years) (usegalaxy.eu): 6384
  • Tool usage (all time) - (usegalaxy.eu): 6409
  • No. of tool users (5 years) (usegalaxy.org): - 101752
  • No. of tool users (all time) (usegalaxy.org): 101752
  • Tool - usage (5 years) (usegalaxy.org): 4662
  • Tool usage (all time) - (usegalaxy.org): 4662
  • No. of tool users (5 years) (usegalaxy.org.au): - 53562
  • No. of tool users (all time) (usegalaxy.org.au): - 53562
  • Tool usage (5 years) (usegalaxy.org.au): 1663
  • Tool - usage (all time) (usegalaxy.org.au): 1663
  • No. of tool users - (5 years) - all main servers: 426681
  • No. of tool users - (all time) - all main servers: 427100
  • Tool usage (5 years) - - all main servers: 12709
  • Tool usage (all time) - all main - servers: 12734
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: Kraken2 for taxonomic designation. title_md: kraken2 - - description_md: '
  • Galaxy tool ids: Kraken2Tax
  • Description: - Convert Kraken output to Galaxy taxonomy data.
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: https://bitbucket.org/natefoo/taxonomy
  • ToolShed - categories: Metagenomics
  • ToolShed id: kraken2tax
  • Date - of first commit of the suite: 2015-08-05
  • Galaxy wrapper - owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax
  • Galaxy - wrapper version: 1.2+galaxy0
  • Conda id: gawk
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 23008
  • No. of tool users (all time) (usegalaxy.eu): 23014
  • Tool - usage (5 years) (usegalaxy.eu): 1060
  • Tool usage (all time) - (usegalaxy.eu): 1061
  • No. of tool users (5 years) (usegalaxy.org): - 16194
  • No. of tool users (all time) (usegalaxy.org): 24490
  • Tool - usage (5 years) (usegalaxy.org): 1719
  • Tool usage (all time) - (usegalaxy.org): 2168
  • No. of tool users (5 years) (usegalaxy.org.au): - 14898
  • No. of tool users (all time) (usegalaxy.org.au): - 14898
  • Tool usage (5 years) (usegalaxy.org.au): 436
  • Tool - usage (all time) (usegalaxy.org.au): 436
  • No. of tool users - (5 years) - all main servers: 54100
  • No. of tool users (all - time) - all main servers: 62402
  • Tool usage (5 years) - - all main servers: 3215
  • Tool usage (all time) - all main - servers: 3665
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: Convert Kraken output to Galaxy taxonomy data. title_md: kraken2tax - - description_md: '
  • Galaxy tool ids: kraken_biom
  • Description: - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: Up-to-date
  • Source: https://github.com/smdabdoub/kraken-biom
  • ToolShed - categories: Metagenomics
  • ToolShed id: kraken_biom
  • Date - of first commit of the suite: 2022-09-03
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/smdabdoub/kraken-biom
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom
  • Galaxy - wrapper version: 1.2.0
  • Conda id: kraken-biom
  • Conda - version: 1.2.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 3185
  • No. of tool - users (all time) (usegalaxy.eu): 3185
  • Tool usage (5 years) - (usegalaxy.eu): 495
  • Tool usage (all time) (usegalaxy.eu): - 495
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 385
  • No. - of tool users (all time) (usegalaxy.org.au): 385
  • Tool usage - (5 years) (usegalaxy.org.au): 48
  • Tool usage (all time) - (usegalaxy.org.au): 48
  • No. of tool users (5 years) - all - main servers: 3570
  • No. of tool users (all time) - all main - servers: 3570
  • Tool usage (5 years) - all main servers: - 543
  • Tool usage (all time) - all main servers: 543
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Create BIOM-format tables (http://biom-format.org) from Kraken + output (http://ccb.jhu.edu/software/kraken/) title_md: kraken_biom - - description_md: '
  • Galaxy tool ids: kraken_taxonomy_report
  • Description: - Kraken taxonomy report
  • bio.tool id: Kraken-Taxonomy-Report
  • bio.tool - ids: Kraken-Taxonomy-Report
  • biii: nan
  • bio.tool - name: Kraken-Taxonomy-Report
  • bio.tool description: - view report of classification for multiple samples
  • EDAM operation: - Visualisation, Classification
  • EDAM topic: Metagenomics, - Taxonomy
  • Status: To update
  • Source: - https://github.com/blankenberg/Kraken-Taxonomy-Report
  • ToolShed - categories: Metagenomics
  • ToolShed id: kraken_taxonomy_report
  • Date - of first commit of the suite: 2016-06-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report
  • Galaxy - wrapper version: 0.0.3
  • Conda id: biopython
  • Conda - version: 1.70
  • EDAM operation (no superclasses): - Visualisation, Classification
  • EDAM topic (no superclasses): - Metagenomics, Taxonomy
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 3981
  • No. of tool users (all time) (usegalaxy.eu): 3986
  • Tool - usage (5 years) (usegalaxy.eu): 769
  • Tool usage (all time) - (usegalaxy.eu): 771
  • No. of tool users (5 years) (usegalaxy.org): - 4087
  • No. of tool users (all time) (usegalaxy.org): 5610
  • Tool - usage (5 years) (usegalaxy.org): 991
  • Tool usage (all time) - (usegalaxy.org): 1284
  • No. of tool users (5 years) (usegalaxy.org.au): - 88
  • No. of tool users (all time) (usegalaxy.org.au): 88
  • Tool - usage (5 years) (usegalaxy.org.au): 41
  • Tool usage (all - time) (usegalaxy.org.au): 41
  • No. of tool users (5 years) - - all main servers: 8156
  • No. of tool users (all time) - - all main servers: 9684
  • Tool usage (5 years) - all main - servers: 1801
  • Tool usage (all time) - all main servers: - 2096
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Kraken taxonomy report title_md: kraken_taxonomy_report - - description_md: '
  • Galaxy tool ids: krakentools_alpha_diversity, - krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, - krakentools_kreport2krona, krakentools_kreport2mpa
  • Description: - KrakenTools is a suite of scripts to be used alongside the Kraken
  • bio.tool - id: krakentools
  • bio.tool ids: krakentools
  • biii: - nan
  • bio.tool name: KrakenTools
  • bio.tool description: - KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq - output files
  • EDAM operation: Visualisation, Aggregation
  • EDAM - topic: Taxonomy, Metagenomics
  • Status: Up-to-date
  • Source: - https://github.com/jenniferlu717/KrakenTools
  • ToolShed categories: - Metagenomics
  • ToolShed id: krakentools
  • Date - of first commit of the suite: 2023-01-13
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools
  • Galaxy - wrapper version: 1.2
  • Conda id: krakentools
  • Conda - version: 1.2
  • EDAM operation (no superclasses): Visualisation, - Aggregation
  • EDAM topic (no superclasses): Taxonomy, Metagenomics
  • Available - on UseGalaxy.org (Main): 6
  • Available on UseGalaxy.org.au: - 6
  • Available on UseGalaxy.eu: 6
  • Available - on UseGalaxy.fr: 6
  • Tools available on UseGalaxy.org (Main): - 6
  • Tools available on UseGalaxy.org.au: 6
  • Tools - available on UseGalaxy.eu: 6
  • Tools available on UseGalaxy.fr: - 6
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 48516
  • No. of tool - users (all time) (usegalaxy.eu): 48516
  • Tool usage (5 years) - (usegalaxy.eu): 2373
  • Tool usage (all time) (usegalaxy.eu): - 2373
  • No. of tool users (5 years) (usegalaxy.org): 8787
  • No. - of tool users (all time) (usegalaxy.org): 8787
  • Tool usage - (5 years) (usegalaxy.org): 943
  • Tool usage (all time) (usegalaxy.org): - 943
  • No. of tool users (5 years) (usegalaxy.org.au): 4369
  • No. - of tool users (all time) (usegalaxy.org.au): 4369
  • Tool - usage (5 years) (usegalaxy.org.au): 393
  • Tool usage (all - time) (usegalaxy.org.au): 393
  • No. of tool users (5 years) - - all main servers: 61672
  • No. of tool users (all time) - - all main servers: 61672
  • Tool usage (5 years) - all main - servers: 3709
  • Tool usage (all time) - all main servers: - 3709
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: KrakenTools is a suite of scripts to be used alongside the Kraken title_md: krakentools - - description_md: '
  • Galaxy tool ids: krocus
  • Description: - Predict MLST directly from uncorrected long reads
  • bio.tool id: - krocus
  • bio.tool ids: krocus
  • biii: - nan
  • bio.tool name: krocus
  • bio.tool description: - Predict MLST directly from uncorrected long reads
  • EDAM operation: - Multilocus sequence typing, k-mer counting
  • EDAM topic: - Public health and epidemiology
  • Status: To update
  • Source: - https://github.com/quadram-institute-bioscience/krocus
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: krocus
  • Date - of first commit of the suite: 2019-09-03
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus
  • Galaxy - wrapper version: 1.0.1
  • Conda id: krocus
  • Conda - version: 1.0.3
  • EDAM operation (no superclasses): - Multilocus sequence typing, k-mer counting
  • EDAM topic (no superclasses): - Public health and epidemiology
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Predict MLST directly from uncorrected long reads title_md: krocus - - description_md: '
  • Galaxy tool ids: lca1
  • Description: - Find lowest diagnostic rank
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://bitbucket.org/natefoo/taxonomy
  • ToolShed categories: - Metagenomics
  • ToolShed id: lca_wrapper
  • Date - of first commit of the suite: 2014-01-27
  • Galaxy wrapper - owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper
  • Galaxy - wrapper version: 1.0.1
  • Conda id: taxonomy
  • Conda - version: 0.10.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 89
  • No. of tool - users (all time) (usegalaxy.eu): 137
  • Tool usage (5 years) - (usegalaxy.eu): 4
  • Tool usage (all time) (usegalaxy.eu): - 20
  • No. of tool users (5 years) (usegalaxy.org): 118
  • No. - of tool users (all time) (usegalaxy.org): 6136
  • Tool usage - (5 years) (usegalaxy.org): 15
  • Tool usage (all time) (usegalaxy.org): - 1112
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 207
  • No. - of tool users (all time) - all main servers: 6273
  • Tool - usage (5 years) - all main servers: 19
  • Tool usage (all - time) - all main servers: 1132
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Find lowest diagnostic rank title_md: lca_wrapper - - description_md: '
  • Galaxy tool ids: legsta
  • Description: - Performs in silico Legionella pneumophila sequence based typing.
  • bio.tool - id: legsta
  • bio.tool ids: legsta
  • biii: - nan
  • bio.tool name: legsta
  • bio.tool description: - Performs in silico Legionella pneumophila sequence based typing
  • EDAM - operation: Sequence analysis
  • EDAM topic: Public - health and epidemiology
  • Status: Up-to-date
  • Source: - https://github.com/tseemann/legsta
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: legsta
  • Date - of first commit of the suite: 2022-02-21
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/tseemann/legsta
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta
  • Galaxy - wrapper version: 0.5.1
  • Conda id: legsta
  • Conda - version: 0.5.1
  • EDAM operation (no superclasses): - Sequence analysis
  • EDAM topic (no superclasses): Public - health and epidemiology
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 92
  • No. of tool users (all time) (usegalaxy.eu): 92
  • Tool - usage (5 years) (usegalaxy.eu): 8
  • Tool usage (all time) - (usegalaxy.eu): 8
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 92
  • No. of tool users (all time) - all main - servers: 92
  • Tool usage (5 years) - all main servers: - 8
  • Tool usage (all time) - all main servers: 8
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Performs in silico Legionella pneumophila sequence based typing. title_md: legsta - - description_md: '
  • Galaxy tool ids: lighter
  • Description: - Lighter is a kmer-based error correction method for whole genome sequencing - data
  • bio.tool id: lighter
  • bio.tool ids: - lighter
  • biii: nan
  • bio.tool name: Lighter
  • 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.
  • EDAM operation: k-mer - counting, Sequence read processing, Sequencing quality control, Sequencing error - detection
  • EDAM topic: Sequencing, Whole genome sequencing, - DNA, Genomics
  • Status: To update
  • Source: - https://github.com/mourisl/Lighter
  • ToolShed categories: - Sequence Analysis, Fasta Manipulation
  • ToolShed id: lighter
  • Date - of first commit of the suite: 2016-06-04
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/lighter
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/lighter
  • Galaxy - wrapper version: 1.0
  • Conda id: lighter
  • Conda - version: 1.1.3
  • EDAM operation (no superclasses): - k-mer counting, Sequence read processing, Sequencing quality control, Sequencing - error detection
  • EDAM topic (no superclasses): Whole genome - sequencing, DNA, Genomics
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 149
  • No. of tool users (all time) (usegalaxy.eu): 171
  • Tool - usage (5 years) (usegalaxy.eu): 27
  • Tool usage (all time) - (usegalaxy.eu): 30
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 149
  • No. of tool users (all time) - all main - servers: 171
  • Tool usage (5 years) - all main servers: - 27
  • Tool usage (all time) - all main servers: 30
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Lighter is a kmer-based error correction method for whole genome + sequencing data title_md: lighter - - description_md: '
  • Galaxy tool ids: limma_voom
  • Description: - Perform RNA-Seq differential expression analysis using limma voom pipeline
  • bio.tool - id: limma
  • bio.tool ids: limma
  • biii: - nan
  • bio.tool name: limma
  • bio.tool description: - Data analysis, linear models and differential expression for microarray data.
  • EDAM - operation: RNA-Seq analysis
  • EDAM topic: Molecular - biology, Genetics
  • Status: Up-to-date
  • Source: - http://bioconductor.org/packages/release/bioc/html/limma.html
  • ToolShed - categories: Transcriptomics, RNA, Statistics
  • ToolShed id: - limma_voom
  • Date of first commit of the suite: 2019-02-17
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom
  • Galaxy - wrapper version: 3.58.1
  • Conda id: bioconductor-limma
  • Conda - version: 3.58.1
  • EDAM operation (no superclasses): - RNA-Seq analysis
  • EDAM topic (no superclasses): Molecular - biology, Genetics
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 23442
  • No. of tool - users (all time) (usegalaxy.eu): 24466
  • Tool usage (5 years) - (usegalaxy.eu): 2379
  • Tool usage (all time) (usegalaxy.eu): - 2475
  • No. of tool users (5 years) (usegalaxy.org): 45734
  • No. - of tool users (all time) (usegalaxy.org): 49342
  • Tool usage - (5 years) (usegalaxy.org): 4565
  • Tool usage (all time) (usegalaxy.org): - 5032
  • No. of tool users (5 years) (usegalaxy.org.au): 9327
  • No. - of tool users (all time) (usegalaxy.org.au): 9517
  • Tool - usage (5 years) (usegalaxy.org.au): 835
  • Tool usage (all - time) (usegalaxy.org.au): 842
  • No. of tool users (5 years) - - all main servers: 78503
  • No. of tool users (all time) - - all main servers: 83325
  • Tool usage (5 years) - all main - servers: 7779
  • Tool usage (all time) - all main servers: - 8349
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Perform RNA-Seq differential expression analysis using limma voom + pipeline title_md: limma_voom - - description_md: '
  • Galaxy tool ids: lineagespot
  • Description: - Identification of SARS-CoV-2 related metagenomic mutations based on a single - (or a list of) variant(s) file(s)
  • bio.tool id: lineagespot
  • bio.tool - ids: lineagespot
  • biii: nan
  • bio.tool - name: lineagespot
  • 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).
  • EDAM - operation: Variant calling
  • EDAM topic: Metagenomics, - Gene transcripts, Evolutionary biology, Sequencing, Genetic variation
  • Status: - To update
  • Source: https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html
  • ToolShed - categories: Metagenomics, Sequence Analysis
  • ToolShed id: - lineagespot
  • Date of first commit of the suite: 2023-07-05
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot
  • Galaxy - wrapper version: 1.6.0
  • Conda id: r-base
  • Conda - version: nan
  • EDAM operation (no superclasses): Variant - calling
  • EDAM topic (no superclasses): Metagenomics, Gene - transcripts, Evolutionary biology, Sequencing, Genetic variation
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 39
  • No. of tool - users (all time) (usegalaxy.eu): 39
  • Tool usage (5 years) - (usegalaxy.eu): 4
  • Tool usage (all time) (usegalaxy.eu): - 4
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 39
  • No. - of tool users (all time) - all main servers: 39
  • Tool usage - (5 years) - all main servers: 4
  • Tool usage (all time) - - all main servers: 4
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Identification of SARS-CoV-2 related metagenomic mutations based + on a single (or a list of) variant(s) file(s) title_md: lineagespot - - description_md: '
  • Galaxy tool ids: lorikeet_spoligotype
  • Description: - Tools for M. tuberculosis DNA fingerprinting (spoligotyping)
  • bio.tool - id: lorikeet
  • bio.tool ids: lorikeet
  • biii: - nan
  • bio.tool name: lorikeet
  • bio.tool description: - Tools for M. tuberculosis DNA fingerprinting (spoligotyping)
  • EDAM - operation: Sequence analysis, Genotyping
  • EDAM topic: - Genotype and phenotype
  • Status: Up-to-date
  • Source: - https://github.com/AbeelLab/lorikeet
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: lorikeet_spoligotype
  • Date - of first commit of the suite: 2018-05-07
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/AbeelLab/lorikeet
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet
  • Galaxy - wrapper version: 20
  • Conda id: lorikeet
  • Conda - version: 20
  • EDAM operation (no superclasses): Sequence - analysis, Genotyping
  • EDAM topic (no superclasses): Genotype - and phenotype
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 822
  • No. of tool - users (all time) (usegalaxy.eu): 822
  • Tool usage (5 years) - (usegalaxy.eu): 14
  • Tool usage (all time) (usegalaxy.eu): - 14
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 822
  • No. - of tool users (all time) - all main servers: 822
  • Tool usage - (5 years) - all main servers: 14
  • Tool usage (all time) - - all main servers: 14
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Tools for M. tuberculosis DNA fingerprinting (spoligotyping) title_md: lorikeet - - description_md: '
  • Galaxy tool ids: lotus2
  • Description: - LotuS2 OTU processing pipeline
  • bio.tool id: lotus2
  • bio.tool - ids: lotus2
  • biii: nan
  • bio.tool name: - lotus2
  • 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.
  • EDAM operation: Sequence feature detection, - DNA barcoding
  • EDAM topic: Metagenomics, Taxonomy, Microbial - ecology
  • Status: To update
  • Source: - http://lotus2.earlham.ac.uk/
  • ToolShed categories: Metagenomics
  • ToolShed - id: lotus2
  • Date of first commit of the suite: 2021-06-08
  • Galaxy - wrapper owner: earlhaminst
  • Galaxy wrapper source: - https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2
  • Galaxy - wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2
  • Galaxy - wrapper version: 2.32
  • Conda id: lotus2
  • Conda - version: 2.34.1
  • EDAM operation (no superclasses): - Sequence feature detection, DNA barcoding
  • EDAM topic (no superclasses): - Metagenomics, Taxonomy, Microbial ecology
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1219
  • No. of tool users (all time) (usegalaxy.eu): 1219
  • Tool - usage (5 years) (usegalaxy.eu): 182
  • Tool usage (all time) - (usegalaxy.eu): 182
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 37
  • No. of tool users (all time) (usegalaxy.org.au): 37
  • Tool - usage (5 years) (usegalaxy.org.au): 4
  • Tool usage (all time) - (usegalaxy.org.au): 4
  • No. of tool users (5 years) - all - main servers: 1256
  • No. of tool users (all time) - all main - servers: 1256
  • Tool usage (5 years) - all main servers: - 186
  • Tool usage (all time) - all main servers: 186
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: LotuS2 OTU processing pipeline title_md: lotus2 - - description_md: '
  • Galaxy tool ids: m6anet
  • Description: - m6anet to detect m6A RNA modifications from nanopore data
  • bio.tool - id: m6Anet
  • bio.tool ids: m6Anet
  • biii: - nan
  • bio.tool name: m6Anet
  • bio.tool description: - Detection of m6A from direct RNA sequencing using a Multiple Instance Learning - framework.
  • EDAM operation: Quantification, Imputation, - Gene expression profiling
  • EDAM topic: RNA-Seq, Transcriptomics, - RNA, Machine learning
  • Status: Up-to-date
  • Source: - https://m6anet.readthedocs.io/en/latest
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: m6anet
  • Date - of first commit of the suite: 2023-10-25
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet
  • Galaxy - wrapper version: 2.1.0
  • Conda id: m6anet
  • Conda - version: 2.1.0
  • EDAM operation (no superclasses): - Quantification, Imputation, Gene expression profiling
  • EDAM topic - (no superclasses): RNA-Seq, Transcriptomics, RNA, Machine learning
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 44
  • No. of tool - users (all time) (usegalaxy.eu): 44
  • Tool usage (5 years) - (usegalaxy.eu): 11
  • Tool usage (all time) (usegalaxy.eu): - 11
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 44
  • No. - of tool users (all time) - all main servers: 44
  • Tool usage - (5 years) - all main servers: 11
  • Tool usage (all time) - - all main servers: 11
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: m6anet to detect m6A RNA modifications from nanopore data title_md: m6anet - - description_md: "
  • Galaxy tool ids: maaslin2
  • Description:\ - \ MaAsLin2 is comprehensive R package for efficiently determining multivariable\ - \ association between microbial meta'omic features and clinical metadata.
  • bio.tool\ - \ id: maaslin2
  • bio.tool ids: maaslin2
  • biii:\ - \ nan
  • bio.tool name: MaAsLin2
  • 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.
  • EDAM operation: Filtering, Statistical calculation,\ - \ Standardisation and normalisation, Visualisation
  • EDAM topic:\ - \ Metagenomics, Statistics and probability
  • Status: Up-to-date
  • Source:\ - \ http://huttenhower.sph.harvard.edu/maaslin
  • ToolShed categories:\ - \ Metagenomics
  • ToolShed id: maaslin2
  • Date\ - \ of first commit of the suite: 2021-11-05
  • Galaxy wrapper\ - \ owner: iuc
  • Galaxy wrapper source: https://github.com/biobakery/Maaslin2
  • Galaxy\ - \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2
  • Galaxy\ - \ wrapper version: 1.18.0
  • Conda id: bioconductor-maaslin2
  • Conda\ - \ version: 1.18.0
  • EDAM operation (no superclasses):\ - \ Filtering, Standardisation and normalisation, Visualisation
  • EDAM\ - \ topic (no superclasses): Metagenomics, Statistics and probability
  • Available\ - \ on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au:\ - \ 0
  • Available on UseGalaxy.eu: 1
  • Available\ - \ on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main):\ - \ 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools\ - \ available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr:\ - \ 0
  • Tools available on APOSTL: 0
  • Tools available\ - \ on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools\ - \ available on ChemFlow: 0
  • Tools available on Coloc-stats:\ - \ 0
  • Tools available on CropGalaxy: 0
  • Tools\ - \ available on Dintor: 0
  • Tools available on GASLINI:\ - \ 0
  • Tools available on Galaxy@AuBi: 0
  • Tools\ - \ available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr:\ - \ 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools\ - \ available on GigaGalaxy: 0
  • Tools available on HyPhy HIV\ - \ NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite:\ - \ 0
  • Tools available on ImmPort Galaxy: 0
  • Tools\ - \ available on InteractoMIX: 0
  • Tools available on MISSISSIPPI:\ - \ 0
  • Tools available on Mandoiu Lab: 0
  • Tools\ - \ available on MiModD NacreousMap: 0
  • Tools available on\ - \ Oqtans: 0
  • Tools available on Palfinder: 0
  • Tools\ - \ available on PepSimili: 0
  • Tools available on PhagePromotor:\ - \ 0
  • Tools available on UseGalaxy.be: 0
  • Tools\ - \ available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no:\ - \ 0
  • Tools available on Viral Variant Visualizer (VVV):\ - \ 0
  • No. of tool users (5 years) (usegalaxy.eu): 2835
  • No.\ - \ of tool users (all time) (usegalaxy.eu): 2835
  • Tool usage\ - \ (5 years) (usegalaxy.eu): 59
  • Tool usage (all time) (usegalaxy.eu):\ - \ 59
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No.\ - \ of tool users (all time) (usegalaxy.org): 0
  • Tool usage\ - \ (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org):\ - \ 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No.\ - \ of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage\ - \ (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time)\ - \ (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all\ - \ main servers: 2835
  • No. of tool users (all time) - all\ - \ main servers: 2835
  • Tool usage (5 years) - all main servers:\ - \ 59
  • Tool usage (all time) - all main servers: 59
  • Reviewed:\ - \ True
  • To keep: True
  • Deprecated: False
" + - description_md: MaAsLin2 is comprehensive R package for efficiently determining + multivariable association between microbial meta'omic features and clinical + metadata. title_md: maaslin2 - - description_md: '
  • Galaxy tool ids: rbc_mafft_add, rbc_mafft
  • Description: - Multiple alignment program for amino acid or nucleotide sequences
  • bio.tool - id: MAFFT
  • bio.tool ids: MAFFT
  • biii: - nan
  • bio.tool name: MAFFT
  • bio.tool description: - MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple - sequence alignment program.
  • EDAM operation: Multiple sequence - alignment
  • EDAM topic: Sequence analysis
  • Status: - To update
  • Source: https://mafft.cbrc.jp/alignment/software/
  • ToolShed - categories: RNA
  • ToolShed id: mafft
  • Date - of first commit of the suite: 2023-11-06
  • Galaxy wrapper - owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/mafft
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/mafft
  • Galaxy - wrapper version: 7.526
  • Conda id: mafft
  • Conda - version: 7.525
  • EDAM operation (no superclasses): - Multiple sequence alignment
  • EDAM topic (no superclasses): - Sequence analysis
  • Available on UseGalaxy.org (Main): 2
  • Available - on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: - 2
  • Available on UseGalaxy.fr: 2
  • Tools available - on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: - 2
  • Tools available on UseGalaxy.eu: 2
  • Tools - available on UseGalaxy.fr: 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: 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 172433
  • No. of tool - users (all time) (usegalaxy.eu): 174456
  • Tool usage (5 years) - (usegalaxy.eu): 1865
  • Tool usage (all time) (usegalaxy.eu): - 1951
  • No. of tool users (5 years) (usegalaxy.org): 108640
  • No. - of tool users (all time) (usegalaxy.org): 122790
  • Tool usage - (5 years) (usegalaxy.org): 4266
  • Tool usage (all time) (usegalaxy.org): - 5521
  • No. of tool users (5 years) (usegalaxy.org.au): 20027
  • No. - of tool users (all time) (usegalaxy.org.au): 20027
  • Tool - usage (5 years) (usegalaxy.org.au): 1172
  • Tool usage (all - time) (usegalaxy.org.au): 1172
  • No. of tool users (5 years) - - all main servers: 301100
  • No. of tool users (all time) - - all main servers: 317273
  • Tool usage (5 years) - all main - servers: 7303
  • Tool usage (all time) - all main servers: - 8644
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Multiple alignment program for amino acid or nucleotide sequences title_md: mafft - - description_md: '
  • Galaxy tool ids: make_nr
  • Description: - Make a FASTA file non-redundant
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr
  • ToolShed - categories: Fasta Manipulation, Sequence Analysis
  • ToolShed - id: make_nr
  • Date of first commit of the suite: 2018-11-06
  • Galaxy - wrapper owner: peterjc
  • Galaxy wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr
  • Galaxy - wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr
  • Galaxy - wrapper version: 0.0.3
  • Conda id: biopython
  • Conda - version: 1.70
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Make a FASTA file non-redundant title_md: make_nr - - description_md: "
  • Galaxy tool ids: maker, maker_map_ids
  • 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.
  • bio.tool\ - \ id: maker
  • bio.tool ids: maker
  • biii:\ - \ nan
  • bio.tool name: MAKER
  • 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.
  • EDAM\ - \ operation: Genome annotation
  • EDAM topic: Genomics,\ - \ DNA, Sequence analysis
  • Status: To update
  • Source:\ - \ http://www.yandell-lab.org/software/maker.html
  • ToolShed categories:\ - \ Sequence Analysis
  • ToolShed id: nan
  • Date\ - \ of first commit of the suite: 2017-10-13
  • Galaxy wrapper\ - \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker
  • Galaxy\ - \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker
  • Galaxy\ - \ wrapper version: 2.31.11
  • Conda id: maker
  • Conda\ - \ version: 3.01.03
  • EDAM operation (no superclasses):\ - \ Genome annotation
  • EDAM topic (no superclasses): Genomics,\ - \ DNA, Sequence analysis
  • Available on UseGalaxy.org (Main):\ - \ 2
  • Available on UseGalaxy.org.au: 2
  • Available\ - \ on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr:\ - \ 2
  • Tools available on UseGalaxy.org (Main): 2
  • Tools\ - \ available on UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu:\ - \ 2
  • Tools available on UseGalaxy.fr: 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: 0
  • Tools available on IPK Galaxy Blast Suite:\ - \ 0
  • Tools available on ImmPort Galaxy: 0
  • Tools\ - \ available on InteractoMIX: 0
  • Tools available on MISSISSIPPI:\ - \ 0
  • Tools available on Mandoiu Lab: 0
  • Tools\ - \ available on MiModD NacreousMap: 0
  • Tools 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.no:\ - \ 2
  • Tools available on Viral Variant Visualizer (VVV):\ - \ 0
  • No. of tool users (5 years) (usegalaxy.eu): 6417
  • No.\ - \ of tool users (all time) (usegalaxy.eu): 6861
  • Tool usage\ - \ (5 years) (usegalaxy.eu): 1315
  • Tool usage (all time)\ - \ (usegalaxy.eu): 1366
  • No. of tool users (5 years) (usegalaxy.org):\ - \ 7235
  • No. of tool users (all time) (usegalaxy.org): 7235
  • Tool\ - \ usage (5 years) (usegalaxy.org): 1858
  • Tool usage (all\ - \ time) (usegalaxy.org): 1858
  • No. of tool users (5 years)\ - \ (usegalaxy.org.au): 4112
  • No. of tool users (all time)\ - \ (usegalaxy.org.au): 4112
  • Tool usage (5 years) (usegalaxy.org.au):\ - \ 902
  • Tool usage (all time) (usegalaxy.org.au): 902
  • No.\ - \ of tool users (5 years) - all main servers: 17764
  • No.\ - \ of tool users (all time) - all main servers: 18208
  • Tool\ - \ usage (5 years) - all main servers: 4075
  • Tool usage (all\ - \ time) - all main servers: 4126
  • Reviewed: True
  • To\ - \ keep: True
  • Deprecated: False
" + - description_md: 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. title_md: maker - - description_md: '
  • Galaxy tool ids: mapseq
  • Description: - fast and accurate sequence read classification tool designed to assign taxonomy - and OTU classifications to ribosomal RNA sequences.
  • bio.tool id: - mapseq
  • bio.tool ids: mapseq
  • biii: - nan
  • bio.tool name: MAPseq
  • bio.tool description: - Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis - .
  • EDAM operation: k-mer counting
  • EDAM topic: - Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, - features and motifs
  • Status: To update
  • Source: - https://github.com/jfmrod/MAPseq
  • ToolShed categories: Metagenomics
  • ToolShed - id: mapseq
  • Date of first commit of the suite: 2023-08-02
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq
  • Galaxy - wrapper version: 2.1.1b
  • Conda id: perl
  • Conda - version: nan
  • EDAM operation (no superclasses): k-mer - counting
  • EDAM topic (no superclasses): Functional, regulatory - and non-coding RNA, Sequence analysis, Sequence sites, features and motifs
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 7871
  • No. of tool - users (all time) (usegalaxy.eu): 7871
  • Tool usage (5 years) - (usegalaxy.eu): 32
  • Tool usage (all time) (usegalaxy.eu): - 32
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 7871
  • No. - of tool users (all time) - all main servers: 7871
  • Tool - usage (5 years) - all main servers: 32
  • Tool usage (all - time) - all main servers: 32
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: fast and accurate sequence read classification tool designed to + assign taxonomy and OTU classifications to ribosomal RNA sequences. title_md: mapseq - - description_md: '
  • Galaxy tool ids: mash_screen, mash_sketch
  • Description: - Fast genome and metagenome distance estimation using MinHash
  • bio.tool - id: mash
  • bio.tool ids: mash
  • biii: - nan
  • bio.tool name: Mash
  • bio.tool description: - Fast genome and metagenome distance estimation using MinHash.
  • EDAM - operation: Sequence distance matrix generation
  • EDAM topic: - Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation
  • Status: - Up-to-date
  • Source: https://github.com/marbl/Mash
  • ToolShed - categories: Metagenomics
  • ToolShed id: nan
  • Date - of first commit of the suite: 2019-01-23
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash
  • Galaxy - wrapper version: 2.3
  • Conda id: mash
  • Conda - version: 2.3
  • EDAM operation (no superclasses): Sequence - distance matrix generation
  • EDAM topic (no superclasses): - Metagenomics, Statistics and probability, Sequence analysis, DNA mutation
  • Available - on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: - 2
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: - 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 10119
  • No. of tool - users (all time) (usegalaxy.eu): 10119
  • Tool usage (5 years) - (usegalaxy.eu): 61
  • Tool usage (all time) (usegalaxy.eu): - 61
  • No. of tool users (5 years) (usegalaxy.org): 19
  • No. - of tool users (all time) (usegalaxy.org): 19
  • Tool usage - (5 years) (usegalaxy.org): 9
  • Tool usage (all time) (usegalaxy.org): - 9
  • No. of tool users (5 years) (usegalaxy.org.au): 647
  • No. - of tool users (all time) (usegalaxy.org.au): 647
  • Tool usage - (5 years) (usegalaxy.org.au): 7
  • Tool usage (all time) (usegalaxy.org.au): - 7
  • No. of tool users (5 years) - all main servers: 10785
  • No. - of tool users (all time) - all main servers: 10785
  • Tool - usage (5 years) - all main servers: 77
  • Tool usage (all - time) - all main servers: 77
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Fast genome and metagenome distance estimation using MinHash title_md: mash - - description_md: '
  • Galaxy tool ids: maxbin2
  • Description: - clusters metagenomic contigs into bins
  • bio.tool id: maxbin
  • bio.tool - ids: maxbin
  • biii: nan
  • bio.tool name: - MaxBin
  • bio.tool description: Software for binning assembled - metagenomic sequences based on an Expectation-Maximization algorithm.
  • EDAM - operation: Sequence assembly
  • EDAM topic: Metagenomics, - Sequence assembly, Microbiology
  • Status: To update
  • Source: - https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html
  • ToolShed - categories: Metagenomics
  • ToolShed id: maxbin2
  • Date - of first commit of the suite: 2019-10-24
  • Galaxy wrapper - owner: mbernt
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2
  • Galaxy - wrapper version: nan
  • Conda id: maxbin2
  • Conda - version: 2.2.7
  • EDAM operation (no superclasses): - Sequence assembly
  • EDAM topic (no superclasses): Metagenomics, - Sequence assembly, Microbiology
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 2798
  • No. of tool users (all time) (usegalaxy.eu): 2798
  • Tool - usage (5 years) (usegalaxy.eu): 314
  • Tool usage (all time) - (usegalaxy.eu): 314
  • No. of tool users (5 years) (usegalaxy.org): - 2452
  • No. of tool users (all time) (usegalaxy.org): 2452
  • Tool - usage (5 years) (usegalaxy.org): 508
  • Tool usage (all time) - (usegalaxy.org): 508
  • No. of tool users (5 years) (usegalaxy.org.au): - 914
  • No. of tool users (all time) (usegalaxy.org.au): 914
  • Tool - usage (5 years) (usegalaxy.org.au): 89
  • Tool usage (all - time) (usegalaxy.org.au): 89
  • No. of tool users (5 years) - - all main servers: 6164
  • No. of tool users (all time) - - all main servers: 6164
  • Tool usage (5 years) - all main - servers: 911
  • Tool usage (all time) - all main servers: - 911
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: clusters metagenomic contigs into bins title_md: maxbin2 - - description_md: '
  • Galaxy tool ids: maxquant, maxquant_mqpar
  • Description: - wrapper for MaxQuant
  • bio.tool id: maxquant
  • bio.tool - ids: maxquant
  • biii: nan
  • bio.tool name: - MaxQuant
  • bio.tool description: Quantitative proteomics - software package designed for analyzing large mass-spectrometric data sets. - It is specifically aimed at high-resolution MS data.
  • EDAM operation: - Imputation, Visualisation, Protein quantification, Statistical calculation, - Standardisation and normalisation, Heat map generation, Clustering, Principal - component plotting
  • EDAM topic: Proteomics experiment, Proteomics, - Statistics and probability
  • Status: Up-to-date
  • Source: - https://www.maxquant.org/
  • ToolShed categories: Proteomics
  • ToolShed - id: maxquant
  • Date of first commit of the suite: - 2021-08-05
  • Galaxy wrapper owner: galaxyp
  • Galaxy - wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
  • Galaxy - wrapper version: 2.0.3.0
  • Conda id: maxquant
  • Conda - version: 2.0.3.0
  • EDAM operation (no superclasses): - Imputation, Visualisation, Protein quantification, Standardisation and normalisation, - Heat map generation, Clustering
  • EDAM topic (no superclasses): - Proteomics experiment, Proteomics, Statistics and probability
  • Available - on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: - 2
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 6863
  • No. of tool - users (all time) (usegalaxy.eu): 7021
  • Tool usage (5 years) - (usegalaxy.eu): 1251
  • Tool usage (all time) (usegalaxy.eu): - 1264
  • No. of tool users (5 years) (usegalaxy.org): 2798
  • No. - of tool users (all time) (usegalaxy.org): 2798
  • Tool usage - (5 years) (usegalaxy.org): 543
  • Tool usage (all time) (usegalaxy.org): - 543
  • No. of tool users (5 years) (usegalaxy.org.au): 3189
  • No. - of tool users (all time) (usegalaxy.org.au): 3189
  • Tool - usage (5 years) (usegalaxy.org.au): 352
  • Tool usage (all - time) (usegalaxy.org.au): 352
  • No. of tool users (5 years) - - all main servers: 12850
  • No. of tool users (all time) - - all main servers: 13008
  • Tool usage (5 years) - all main - servers: 2146
  • Tool usage (all time) - all main servers: - 2159
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: wrapper for MaxQuant title_md: maxquant - - description_md: '
  • Galaxy tool ids: mcl
  • Description: - The Markov Cluster Algorithm, a cluster algorithm for graphs
  • bio.tool - id: mcl
  • bio.tool ids: mcl
  • biii: - nan
  • bio.tool name: MCL
  • bio.tool description: - MCL is a clustering algorithm widely used in bioinformatics and gaining traction - in other fields.
  • EDAM operation: Clustering, Network analysis, - Gene regulatory network analysis
  • EDAM topic: Molecular - interactions, pathways and networks
  • Status: Up-to-date
  • Source: - https://micans.org/mcl/man/mcl.html
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: mcl
  • Date of - first commit of the suite: 2022-05-12
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/mcl
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl
  • Galaxy - wrapper version: 22.282
  • Conda id: mcl
  • Conda - version: 22.282
  • EDAM operation (no superclasses): - Clustering, Gene regulatory network analysis
  • EDAM topic (no superclasses): - Molecular interactions, pathways and networks
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 35
  • No. of tool users (all time) (usegalaxy.eu): 35
  • Tool - usage (5 years) (usegalaxy.eu): 13
  • Tool usage (all time) - (usegalaxy.eu): 13
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 35
  • No. of tool users (all time) - all main - servers: 35
  • Tool usage (5 years) - all main servers: - 13
  • Tool usage (all time) - all main servers: 13
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: The Markov Cluster Algorithm, a cluster algorithm for graphs title_md: mcl - - description_md: '
  • Galaxy tool ids: medaka_consensus, medaka_consensus_pipeline, - medaka_snp, medaka_variant
  • Description: Sequence correction - provided by ONT Research
  • bio.tool id: medaka
  • bio.tool - ids: medaka
  • biii: nan
  • bio.tool name: - Medaka
  • 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.
  • EDAM operation: Base-calling, - Variant calling, Sequence assembly
  • EDAM topic: Sequence - assembly, Machine learning
  • Status: To update
  • Source: - https://github.com/nanoporetech/medaka
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: nan
  • Date of - first commit of the suite: 2020-08-24
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka
  • Galaxy - wrapper version: 1.7.2
  • Conda id: medaka
  • Conda - version: 2.0.1
  • EDAM operation (no superclasses): - Base-calling, Variant calling, Sequence assembly
  • EDAM topic (no - superclasses): Sequence assembly, Machine learning
  • Available - on UseGalaxy.org (Main): 3
  • Available on UseGalaxy.org.au: - 3
  • Available on UseGalaxy.eu: 3
  • Available - on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): - 3
  • Tools available on UseGalaxy.org.au: 3
  • Tools - available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: - 3
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 3
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 117975
  • No. of tool - users (all time) (usegalaxy.eu): 117975
  • Tool usage (5 years) - (usegalaxy.eu): 1693
  • Tool usage (all time) (usegalaxy.eu): - 1693
  • No. of tool users (5 years) (usegalaxy.org): 55063
  • No. - of tool users (all time) (usegalaxy.org): 55063
  • Tool usage - (5 years) (usegalaxy.org): 796
  • Tool usage (all time) (usegalaxy.org): - 796
  • No. of tool users (5 years) (usegalaxy.org.au): 9325
  • No. - of tool users (all time) (usegalaxy.org.au): 9325
  • Tool - usage (5 years) (usegalaxy.org.au): 639
  • Tool usage (all - time) (usegalaxy.org.au): 639
  • No. of tool users (5 years) - - all main servers: 182363
  • No. of tool users (all time) - - all main servers: 182363
  • Tool usage (5 years) - all main - servers: 3128
  • Tool usage (all time) - all main servers: - 3128
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Sequence correction provided by ONT Research title_md: medaka - - description_md: '
  • Galaxy tool ids: megahit
  • Description: - An ultra-fast single-node solution for large and complex metagenomics assembly - via succinct de Bruijn graph.
  • bio.tool id: megahit
  • bio.tool - ids: megahit
  • biii: nan
  • bio.tool name: - MEGAHIT
  • 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.
  • EDAM operation: Genome - assembly
  • EDAM topic: Metagenomics, Sequencing, Ecology, - Sequence assembly
  • Status: Up-to-date
  • Source: - https://github.com/voutcn/megahit
  • ToolShed categories: - Sequence Analysis, Assembly, Metagenomics
  • ToolShed id: - megahit
  • Date of first commit of the suite: 2017-09-22
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit
  • Galaxy - wrapper version: 1.2.9
  • Conda id: megahit
  • Conda - version: 1.2.9
  • EDAM operation (no superclasses): - Genome assembly
  • EDAM topic (no superclasses): Metagenomics, - Sequencing, Sequence assembly
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 12692
  • No. of tool users (all time) (usegalaxy.eu): 13292
  • Tool - usage (5 years) (usegalaxy.eu): 1349
  • Tool usage (all time) - (usegalaxy.eu): 1400
  • No. of tool users (5 years) (usegalaxy.org): - 16645
  • No. of tool users (all time) (usegalaxy.org): 16645
  • Tool - usage (5 years) (usegalaxy.org): 2140
  • Tool usage (all time) - (usegalaxy.org): 2140
  • No. of tool users (5 years) (usegalaxy.org.au): - 6214
  • No. of tool users (all time) (usegalaxy.org.au): 6214
  • Tool - usage (5 years) (usegalaxy.org.au): 431
  • Tool usage (all - time) (usegalaxy.org.au): 431
  • No. of tool users (5 years) - - all main servers: 35551
  • No. of tool users (all time) - - all main servers: 36151
  • Tool usage (5 years) - all main - servers: 3920
  • Tool usage (all time) - all main servers: - 3971
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: An ultra-fast single-node solution for large and complex metagenomics + assembly via succinct de Bruijn graph. title_md: megahit - - description_md: '
  • Galaxy tool ids: megahit_contig2fastg
  • Description: - A subprogram within the Megahit toolkit for converting contigs to assembly graphs - (fastg)
  • bio.tool id: megahit
  • bio.tool ids: - megahit
  • biii: nan
  • bio.tool name: MEGAHIT
  • 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.
  • EDAM - operation: Genome assembly
  • EDAM topic: Metagenomics, - Sequencing, Ecology, Sequence assembly
  • Status: To update
  • Source: - https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp
  • ToolShed - categories: Sequence Analysis, Assembly, Metagenomics
  • ToolShed - id: megahit_contig2fastg
  • Date of first commit of the suite: - 2018-11-09
  • Galaxy wrapper owner: iuc
  • Galaxy - wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg
  • Galaxy - wrapper version: 1.1.3
  • Conda id: megahit
  • Conda - version: 1.2.9
  • EDAM operation (no superclasses): - Genome assembly
  • EDAM topic (no superclasses): Metagenomics, - Sequencing, Sequence assembly
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 513
  • No. of tool users (all time) (usegalaxy.eu): 557
  • Tool - usage (5 years) (usegalaxy.eu): 152
  • Tool usage (all time) - (usegalaxy.eu): 155
  • No. of tool users (5 years) (usegalaxy.org): - 74
  • No. of tool users (all time) (usegalaxy.org): 74
  • Tool - usage (5 years) (usegalaxy.org): 35
  • Tool usage (all time) - (usegalaxy.org): 35
  • No. of tool users (5 years) (usegalaxy.org.au): - 10
  • No. of tool users (all time) (usegalaxy.org.au): 10
  • Tool - usage (5 years) (usegalaxy.org.au): 4
  • Tool usage (all time) - (usegalaxy.org.au): 4
  • No. of tool users (5 years) - all - main servers: 597
  • No. of tool users (all time) - all main - servers: 641
  • Tool usage (5 years) - all main servers: - 191
  • Tool usage (all time) - all main servers: 194
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: A subprogram within the Megahit toolkit for converting contigs + to assembly graphs (fastg) title_md: megahit_contig2fastg - - description_md: "
  • Galaxy tool ids: megan_blast2lca, megan_blast2rma,\ - \ megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor,\ - \ megan_sam2rma
  • 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).
  • bio.tool\ - \ id: megan
  • bio.tool ids: megan
  • biii:\ - \ nan
  • bio.tool name: MEGAN
  • 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.
  • EDAM\ - \ operation: Sequence analysis, Taxonomic classification
  • EDAM\ - \ topic: Sequence analysis
  • Status: To update
  • Source:\ - \ https://github.com/husonlab/megan-ce
  • ToolShed categories:\ - \ Sequence Analysis
  • ToolShed id: megan
  • Date\ - \ of first commit of the suite: 2021-11-24
  • Galaxy wrapper\ - \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan
  • Galaxy\ - \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan
  • Galaxy\ - \ wrapper version: 6.21.7
  • Conda id: megan
  • Conda\ - \ version: 6.25.9
  • EDAM operation (no superclasses):\ - \ Sequence analysis, Taxonomic classification
  • EDAM topic (no superclasses):\ - \ Sequence analysis
  • Available on UseGalaxy.org (Main):\ - \ 0
  • Available on UseGalaxy.org.au: 0
  • Available\ - \ on UseGalaxy.eu: 7
  • Available on UseGalaxy.fr:\ - \ 0
  • Tools available on UseGalaxy.org (Main): 0
  • Tools\ - \ available on UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu:\ - \ 7
  • Tools available on UseGalaxy.fr: 0
  • Tools\ - \ available on APOSTL: 0
  • Tools available on ARGs-OAP:\ - \ 0
  • Tools available on CIRM-CFBP: 0
  • Tools\ - \ available on ChemFlow: 0
  • Tools available on Coloc-stats:\ - \ 0
  • Tools available on CropGalaxy: 0
  • Tools\ - \ available on Dintor: 0
  • Tools available on GASLINI:\ - \ 0
  • Tools available on Galaxy@AuBi: 0
  • Tools\ - \ available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr:\ - \ 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools\ - \ available on GigaGalaxy: 0
  • Tools available on HyPhy HIV\ - \ NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite:\ - \ 0
  • Tools available on ImmPort Galaxy: 0
  • Tools\ - \ available on InteractoMIX: 0
  • Tools available on MISSISSIPPI:\ - \ 0
  • Tools available on Mandoiu Lab: 0
  • Tools\ - \ available on MiModD NacreousMap: 0
  • Tools available on\ - \ Oqtans: 0
  • Tools available 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.no:\ - \ 0
  • Tools available on Viral Variant Visualizer (VVV):\ - \ 0
  • No. of tool users (5 years) (usegalaxy.eu): 4130
  • No.\ - \ of tool users (all time) (usegalaxy.eu): 4130
  • Tool usage\ - \ (5 years) (usegalaxy.eu): 447
  • Tool usage (all time) (usegalaxy.eu):\ - \ 447
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No.\ - \ of tool users (all time) (usegalaxy.org): 0
  • Tool usage\ - \ (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org):\ - \ 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No.\ - \ of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage\ - \ (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time)\ - \ (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all\ - \ main servers: 4130
  • No. of tool users (all time) - all\ - \ main servers: 4130
  • Tool usage (5 years) - all main servers:\ - \ 447
  • Tool usage (all time) - all main servers: 447
  • Reviewed:\ - \ True
  • To keep: True
  • Deprecated: False
" + - description_md: 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). title_md: megan - - description_md: '
  • Galaxy tool ids: meningotype
  • Description: - Assign sequence type to N. meningitidis genome assemblies
  • bio.tool - id: meningotype
  • bio.tool ids: meningotype
  • biii: - nan
  • bio.tool name: meningotype
  • bio.tool description: - In silico typing of Neisseria meningitidis contigs.
  • EDAM operation: - Genotyping, Multilocus sequence typing
  • EDAM topic: Microbiology, - Genotype and phenotype
  • Status: Up-to-date
  • Source: - https://github.com/MDU-PHL/meningotype
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: meningotype
  • Date - of first commit of the suite: 2023-06-06
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype
  • Galaxy - wrapper version: 0.8.5
  • Conda id: meningotype
  • Conda - version: 0.8.5
  • EDAM operation (no superclasses): - Multilocus sequence typing
  • EDAM topic (no superclasses): - Microbiology, Genotype and phenotype
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Assign sequence type to N. meningitidis genome assemblies title_md: meningotype - - description_md: '
  • Galaxy tool ids: merqury, merquryplot
  • Description: - Merqury is a tool for evaluating genomes assemblies based of k-mer operations.
  • bio.tool - id: merqury
  • bio.tool ids: merqury
  • biii: - nan
  • bio.tool name: Merqury
  • 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.
  • EDAM operation: - Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly
  • EDAM - topic: Sequence assembly, Whole genome sequencing, Plant biology
  • Status: - Up-to-date
  • Source: https://github.com/marbl/merqury
  • ToolShed - categories: Assembly
  • ToolShed id: merqury
  • Date - of first commit of the suite: 2021-04-18
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury
  • Galaxy - wrapper version: 1.3
  • Conda id: merqury
  • Conda - version: 1.3
  • EDAM operation (no superclasses): Genome - assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly
  • EDAM - topic (no superclasses): Sequence assembly, Whole genome sequencing, - Plant biology
  • Available on UseGalaxy.org (Main): 2
  • Available - on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: - 2
  • Available on UseGalaxy.fr: 2
  • Tools available - on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: - 2
  • Tools available on UseGalaxy.eu: 2
  • Tools - available on UseGalaxy.fr: 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 3150
  • No. of tool - users (all time) (usegalaxy.eu): 3150
  • Tool usage (5 years) - (usegalaxy.eu): 477
  • Tool usage (all time) (usegalaxy.eu): - 477
  • No. of tool users (5 years) (usegalaxy.org): 730
  • No. - of tool users (all time) (usegalaxy.org): 730
  • Tool usage - (5 years) (usegalaxy.org): 196
  • Tool usage (all time) (usegalaxy.org): - 196
  • No. of tool users (5 years) (usegalaxy.org.au): 1183
  • No. - of tool users (all time) (usegalaxy.org.au): 1183
  • Tool - usage (5 years) (usegalaxy.org.au): 151
  • Tool usage (all - time) (usegalaxy.org.au): 151
  • No. of tool users (5 years) - - all main servers: 5063
  • No. of tool users (all time) - - all main servers: 5063
  • Tool usage (5 years) - all main - servers: 824
  • Tool usage (all time) - all main servers: - 824
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Merqury is a tool for evaluating genomes assemblies based of k-mer + operations. title_md: merqury - - description_md: '
  • Galaxy tool ids: meryl_arithmetic_kmers, - meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, - meryl_print, meryl_trio_mode
  • Description: Meryl a k-mer - counter.
  • bio.tool id: meryl
  • bio.tool ids: - meryl
  • biii: nan
  • bio.tool name: Meryl
  • 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.
  • EDAM operation: - k-mer counting
  • EDAM topic: Whole genome sequencing, Genomics, - Sequence analysis, Sequencing
  • Status: Up-to-date
  • Source: - https://github.com/marbl/meryl
  • ToolShed categories: Assembly
  • ToolShed - id: meryl
  • Date of first commit of the suite: 2021-04-05
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl
  • Galaxy - wrapper version: 1.3
  • Conda id: merqury
  • Conda - version: 1.3
  • EDAM operation (no superclasses): k-mer - counting
  • EDAM topic (no superclasses): Whole genome sequencing, - Genomics, Sequence analysis
  • Available on UseGalaxy.org (Main): - 7
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 7
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Meryl a k-mer counter. title_md: meryl - - description_md: '
  • Galaxy tool ids: metabat2_jgi_summarize_bam_contig_depths, - metabat2
  • 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.
  • bio.tool id: MetaBAT_2
  • bio.tool - ids: MetaBAT_2
  • biii: nan
  • bio.tool - name: MetaBAT 2
  • 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
  • EDAM operation: - Read binning, Sequence assembly, Genome annotation
  • EDAM topic: - Metagenomics, Sequence assembly, Metagenomic sequencing
  • Status: - To update
  • Source: https://bitbucket.org/berkeleylab/metabat/src/master/
  • ToolShed - categories: Metagenomics
  • ToolShed id: metabat2
  • Date - of first commit of the suite: 2022-01-28
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2
  • Galaxy - wrapper version: 2.15
  • Conda id: metabat2
  • Conda - version: 2.17
  • EDAM operation (no superclasses): - Read binning, Sequence assembly, Genome annotation
  • EDAM topic - (no superclasses): Metagenomics, Sequence assembly, Metagenomic sequencing
  • Available - on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 2
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 6135
  • No. of tool - users (all time) (usegalaxy.eu): 6135
  • Tool usage (5 years) - (usegalaxy.eu): 382
  • Tool usage (all time) (usegalaxy.eu): - 382
  • No. of tool users (5 years) (usegalaxy.org): 881
  • No. - of tool users (all time) (usegalaxy.org): 881
  • Tool usage - (5 years) (usegalaxy.org): 151
  • Tool usage (all time) (usegalaxy.org): - 151
  • No. of tool users (5 years) (usegalaxy.org.au): 1094
  • No. - of tool users (all time) (usegalaxy.org.au): 1094
  • Tool - usage (5 years) (usegalaxy.org.au): 104
  • Tool usage (all - time) (usegalaxy.org.au): 104
  • No. of tool users (5 years) - - all main servers: 8110
  • No. of tool users (all time) - - all main servers: 8110
  • Tool usage (5 years) - all main - servers: 637
  • Tool usage (all time) - all main servers: - 637
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: 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. title_md: metabat2 - - description_md: '
  • Galaxy tool ids: metaeuk_easy_predict
  • 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.
  • bio.tool - id: MetaEuk
  • bio.tool ids: MetaEuk
  • biii: - nan
  • bio.tool name: MetaEuk
  • bio.tool description: - MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale - eukaryotic metagenomics
  • EDAM operation: Homology-based - gene prediction
  • EDAM topic: Metagenomics, Gene and protein - families
  • Status: To update
  • Source: - https://github.com/soedinglab/metaeuk
  • ToolShed categories: - Sequence Analysis, Genome annotation
  • ToolShed id: nan
  • Date - of first commit of the suite: 2020-08-04
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk
  • Galaxy - wrapper version: 7.bba0d80
  • Conda id: metaeuk
  • Conda - version: 6.a5d39d9
  • EDAM operation (no superclasses): - Homology-based gene prediction
  • EDAM topic (no superclasses): - Metagenomics, Gene and protein families
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 312
  • No. of tool users (all time) (usegalaxy.eu): 312
  • Tool - usage (5 years) (usegalaxy.eu): 40
  • Tool usage (all time) - (usegalaxy.eu): 40
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 312
  • No. of tool users (all time) - all main - servers: 312
  • Tool usage (5 years) - all main servers: - 40
  • Tool usage (all time) - all main servers: 40
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: '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. ' title_md: metaeuk - - description_md: '
  • Galaxy tool ids: metagene_annotator
  • Description: - MetaGeneAnnotator gene-finding program for prokaryote and phage
  • bio.tool - id: metageneannotator
  • bio.tool ids: metageneannotator
  • biii: - nan
  • bio.tool name: MetaGeneAnnotator
  • bio.tool - description: Prokaryotic gene finding program from environmental genome - shotgun sequences or metagenomic sequences.
  • EDAM operation: - Sequence annotation
  • EDAM topic: Genomics, Model organisms, - Data submission, annotation and curation
  • Status: Up-to-date
  • Source: - http://metagene.nig.ac.jp/
  • ToolShed categories: Sequence - Analysis
  • ToolShed id: metagene_annotator
  • Date - of first commit of the suite: 2018-03-21
  • Galaxy wrapper - owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator
  • Galaxy - wrapper version: 1.0
  • Conda id: metagene_annotator
  • Conda - version: 1.0
  • EDAM operation (no superclasses): Sequence - annotation
  • EDAM topic (no superclasses): Genomics, Model - organisms, Data submission, annotation and curation
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 980
  • No. of tool - users (all time) (usegalaxy.eu): 980
  • Tool usage (5 years) - (usegalaxy.eu): 323
  • Tool usage (all time) (usegalaxy.eu): - 323
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 980
  • No. - of tool users (all time) - all main servers: 980
  • Tool usage - (5 years) - all main servers: 323
  • Tool usage (all time) - - all main servers: 323
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: MetaGeneAnnotator gene-finding program for prokaryote and phage title_md: metagene_annotator - - description_md: '
  • Galaxy tool ids: metagenomeseq_normalizaton
  • Description: - metagenomeSeq Normalization
  • bio.tool id: metagenomeseq
  • bio.tool - ids: metagenomeseq
  • biii: nan
  • bio.tool - name: metagenomeSeq
  • 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.
  • EDAM operation: Sequence visualisation, - Statistical calculation
  • EDAM topic: Metagenomics, Sequencing
  • Status: - To update
  • Source: https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html
  • ToolShed - categories: Metagenomics
  • ToolShed id: metagenomeseq_normalization
  • Date - of first commit of the suite: 2017-03-27
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq
  • Galaxy - wrapper version: 1.16.0-0.0.1
  • Conda id: bioconductor-metagenomeseq
  • Conda - version: 1.43.0
  • EDAM operation (no superclasses): - Sequence visualisation, Statistical calculation
  • EDAM topic (no - superclasses): Metagenomics, Sequencing
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 556
  • No. of tool users (all time) (usegalaxy.eu): 756
  • Tool - usage (5 years) (usegalaxy.eu): 17
  • Tool usage (all time) - (usegalaxy.eu): 21
  • No. of tool users (5 years) (usegalaxy.org): - 310
  • No. of tool users (all time) (usegalaxy.org): 514
  • Tool - usage (5 years) (usegalaxy.org): 35
  • Tool usage (all time) - (usegalaxy.org): 55
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 866
  • No. of tool users (all time) - all main - servers: 1270
  • Tool usage (5 years) - all main servers: - 52
  • Tool usage (all time) - all main servers: 76
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: metagenomeSeq Normalization title_md: metagenomeseq - - description_md: '
  • Galaxy tool ids: metanovo
  • Description: - Produce targeted databases for mass spectrometry analysis.
  • bio.tool - id: metanovo
  • bio.tool ids: metanovo
  • biii: - nan
  • bio.tool name: MetaNovo
  • bio.tool description: - An open-source pipeline for probabilistic peptide discovery in complex metaproteomic - datasets.
  • EDAM operation: Target-Decoy, de Novo sequencing, - Tag-based peptide identification, Protein identification, Expression analysis
  • EDAM - topic: Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, - Small molecules
  • Status: Up-to-date
  • Source: - https://github.com/uct-cbio/proteomics-pipelines
  • ToolShed categories: - Proteomics
  • ToolShed id: metanovo
  • Date of - first commit of the suite: 2022-03-29
  • Galaxy wrapper owner: - galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo
  • Galaxy - wrapper version: 1.9.4
  • Conda id: metanovo
  • Conda - version: 1.9.4
  • EDAM operation (no superclasses): - Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein - identification, Expression analysis
  • EDAM topic (no superclasses): - Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 4471
  • No. of tool - users (all time) (usegalaxy.eu): 4471
  • Tool usage (5 years) - (usegalaxy.eu): 29
  • Tool usage (all time) (usegalaxy.eu): - 29
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 4471
  • No. - of tool users (all time) - all main servers: 4471
  • Tool - usage (5 years) - all main servers: 29
  • Tool usage (all - time) - all main servers: 29
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Produce targeted databases for mass spectrometry analysis. title_md: metanovo - - description_md: '
  • Galaxy tool ids: customize_metaphlan_database, - extract_metaphlan_database, merge_metaphlan_tables, metaphlan
  • Description: - MetaPhlAn for Metagenomic Phylogenetic Analysis
  • bio.tool id: - metaphlan
  • bio.tool ids: metaphlan
  • biii: - nan
  • bio.tool name: MetaPhlAn
  • bio.tool description: - Computational tool for profiling the composition of microbial communities from - metagenomic shotgun sequencing data.
  • EDAM operation: Nucleic - acid sequence analysis, Phylogenetic tree analysis
  • EDAM topic: - Metagenomics, Phylogenomics
  • Status: Up-to-date
  • Source: - https://github.com/biobakery/MetaPhlAn
  • ToolShed categories: - Metagenomics
  • ToolShed id: metaphlan
  • Date - of first commit of the suite: 2021-04-13
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan
  • Galaxy - wrapper version: 4.1.1
  • Conda id: metaphlan
  • Conda - version: 4.1.1
  • EDAM operation (no superclasses): - Nucleic acid sequence analysis
  • EDAM topic (no superclasses): - Metagenomics, Phylogenomics
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 2
  • Available - on UseGalaxy.eu: 4
  • Available on UseGalaxy.fr: 4
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu: - 4
  • Tools available on UseGalaxy.fr: 4
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 4
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 16629
  • No. of tool users (all time) (usegalaxy.eu): 16648
  • Tool - usage (5 years) (usegalaxy.eu): 1183
  • Tool usage (all time) - (usegalaxy.eu): 1187
  • No. of tool users (5 years) (usegalaxy.org): - 3983
  • No. of tool users (all time) (usegalaxy.org): 3983
  • Tool - usage (5 years) (usegalaxy.org): 572
  • Tool usage (all time) - (usegalaxy.org): 572
  • No. of tool users (5 years) (usegalaxy.org.au): - 4747
  • No. of tool users (all time) (usegalaxy.org.au): 4747
  • Tool - usage (5 years) (usegalaxy.org.au): 278
  • Tool usage (all - time) (usegalaxy.org.au): 278
  • No. of tool users (5 years) - - all main servers: 25359
  • No. of tool users (all time) - - all main servers: 25378
  • Tool usage (5 years) - all main - servers: 2033
  • Tool usage (all time) - all main servers: - 2037
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: MetaPhlAn for Metagenomic Phylogenetic Analysis title_md: metaphlan - - description_md: '
  • Galaxy tool ids: metaquantome_db, metaquantome_expand, - metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz
  • Description: - quantitative analysis of microbiome taxonomy and function
  • bio.tool - id: metaQuantome
  • bio.tool ids: metaQuantome
  • biii: - nan
  • bio.tool name: metaQuantome
  • 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.
  • EDAM - operation: Principal component visualisation, Visualisation, Functional - clustering, Query and retrieval, Differential protein expression analysis, Heat - map generation, Quantification, Indexing, Filtering, Statistical inference
  • EDAM - topic: Proteomics, Metatranscriptomics, Microbial ecology, Proteomics - experiment, Metagenomics
  • Status: Up-to-date
  • Source: - https://github.com/galaxyproteomics/metaquantome/
  • ToolShed categories: - Proteomics
  • ToolShed id: metaquantome
  • Date - of first commit of the suite: 2019-04-05
  • Galaxy wrapper - owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome
  • Galaxy - wrapper version: 2.0.2
  • Conda id: metaquantome
  • Conda - version: 2.0.2
  • EDAM operation (no superclasses): - Principal component visualisation, Functional clustering, Query and retrieval, - Heat map generation, Quantification, Indexing, Filtering, Statistical inference
  • EDAM - topic (no superclasses): Proteomics, Metatranscriptomics, Microbial ecology, - Proteomics experiment, Metagenomics
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 6
  • Available - on UseGalaxy.eu: 6
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 6
  • Tools available on UseGalaxy.eu: - 6
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools 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.no: 6
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 2730
  • No. of tool users (all time) (usegalaxy.eu): 2831
  • Tool - usage (5 years) (usegalaxy.eu): 260
  • Tool usage (all time) - (usegalaxy.eu): 262
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 1540
  • No. of tool users (all time) (usegalaxy.org.au): 1540
  • Tool - usage (5 years) (usegalaxy.org.au): 71
  • Tool usage (all - time) (usegalaxy.org.au): 71
  • No. of tool users (5 years) - - all main servers: 4270
  • No. of tool users (all time) - - all main servers: 4371
  • Tool usage (5 years) - all main - servers: 331
  • Tool usage (all time) - all main servers: - 333
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: quantitative analysis of microbiome taxonomy and function title_md: metaquantome - - description_md: '
  • Galaxy tool ids: metawrapmg_binning
  • Description: - A flexible pipeline for genome-resolved metagenomic data analysis
  • bio.tool - id: metawrap
  • bio.tool ids: metawrap
  • biii: - nan
  • bio.tool name: MetaWRAP
  • 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.
  • EDAM operation: Read binning, - Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing
  • EDAM - topic: Whole genome sequencing, Metagenomic sequencing, Metagenomics
  • Status: - Up-to-date
  • Source: https://github.com/bxlab/metaWRAP
  • ToolShed - categories: Metagenomics
  • ToolShed id: metawrapmg_binning
  • Date - of first commit of the suite: 2024-04-11
  • Galaxy wrapper - owner: galaxy-australia
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg
  • Galaxy - wrapper version: 1.3.0
  • Conda id: metawrap-mg
  • Conda - version: 1.3.0
  • EDAM operation (no superclasses): - Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing
  • EDAM - topic (no superclasses): Whole genome sequencing, Metagenomic sequencing, - Metagenomics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 142
  • No. of tool - users (all time) (usegalaxy.eu): 142
  • Tool usage (5 years) - (usegalaxy.eu): 32
  • Tool usage (all time) (usegalaxy.eu): - 32
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 379
  • No. - of tool users (all time) (usegalaxy.org.au): 379
  • Tool usage - (5 years) (usegalaxy.org.au): 47
  • Tool usage (all time) - (usegalaxy.org.au): 47
  • No. of tool users (5 years) - all - main servers: 521
  • No. of tool users (all time) - all main - servers: 521
  • Tool usage (5 years) - all main servers: - 79
  • Tool usage (all time) - all main servers: 79
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: A flexible pipeline for genome-resolved metagenomic data analysis title_md: metawrapmg - - description_md: '
  • Galaxy tool ids: minia
  • Description: - Short-read assembler based on a de Bruijn graph
  • bio.tool id: - minia
  • bio.tool ids: minia
  • biii: nan
  • bio.tool - name: Minia
  • 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.
  • EDAM operation: Genome assembly
  • EDAM - topic: Sequence assembly
  • Status: Up-to-date
  • Source: - https://gatb.inria.fr/software/minia/
  • ToolShed categories: - Assembly
  • ToolShed id: minia
  • Date of first - commit of the suite: 2020-04-08
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia
  • Galaxy - wrapper version: 3.2.6
  • Conda id: minia
  • Conda - version: 3.2.6
  • EDAM operation (no superclasses): - Genome assembly
  • EDAM topic (no superclasses): Sequence - assembly
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 7116
  • No. of tool - users (all time) (usegalaxy.eu): 7116
  • Tool usage (5 years) - (usegalaxy.eu): 256
  • Tool usage (all time) (usegalaxy.eu): - 256
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 278
  • No. - of tool users (all time) (usegalaxy.org.au): 278
  • Tool usage - (5 years) (usegalaxy.org.au): 60
  • Tool usage (all time) - (usegalaxy.org.au): 60
  • No. of tool users (5 years) - all - main servers: 7394
  • No. of tool users (all time) - all main - servers: 7394
  • Tool usage (5 years) - all main servers: - 316
  • Tool usage (all time) - all main servers: 316
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Short-read assembler based on a de Bruijn graph title_md: minia - - description_md: '
  • Galaxy tool ids: miniasm
  • Description: - Miniasm - Ultrafast de novo assembly for long noisy reads (though having no - consensus step)
  • bio.tool id: miniasm
  • bio.tool - ids: miniasm
  • biii: nan
  • bio.tool name: - miniasm
  • 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.
  • EDAM - operation: De-novo assembly
  • EDAM topic: Genomics, - Sequence assembly
  • Status: To update
  • Source: - https://github.com/lh3/miniasm
  • ToolShed categories: Assembly
  • ToolShed - id: miniasm
  • Date of first commit of the suite: 2019-06-18
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm
  • Galaxy - wrapper version: 0.3_r179
  • Conda id: miniasm
  • Conda - version: 0.3
  • EDAM operation (no superclasses): De-novo - assembly
  • EDAM topic (no superclasses): Genomics, Sequence - assembly
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 13357
  • No. of tool - users (all time) (usegalaxy.eu): 13479
  • Tool usage (5 years) - (usegalaxy.eu): 554
  • Tool usage (all time) (usegalaxy.eu): - 562
  • No. of tool users (5 years) (usegalaxy.org): 8416
  • No. - of tool users (all time) (usegalaxy.org): 8416
  • Tool usage - (5 years) (usegalaxy.org): 448
  • Tool usage (all time) (usegalaxy.org): - 448
  • No. of tool users (5 years) (usegalaxy.org.au): 898
  • No. - of tool users (all time) (usegalaxy.org.au): 898
  • Tool usage - (5 years) (usegalaxy.org.au): 85
  • Tool usage (all time) - (usegalaxy.org.au): 85
  • No. of tool users (5 years) - all - main servers: 22671
  • No. of tool users (all time) - all - main servers: 22793
  • Tool usage (5 years) - all main servers: - 1087
  • Tool usage (all time) - all main servers: 1095
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Miniasm - Ultrafast de novo assembly for long noisy reads (though + having no consensus step) title_md: miniasm - - description_md: '
  • Galaxy tool ids: minipolish
  • Description: - Polishing miniasm assemblies
  • bio.tool id: minipolish
  • bio.tool - ids: minipolish
  • biii: nan
  • bio.tool - name: minipolish
  • 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.
  • EDAM operation: Localised reassembly, Read - depth analysis
  • EDAM topic: Sequence assembly, Sequencing
  • Status: - Up-to-date
  • Source: https://github.com/rrwick/Minipolish
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: minipolish
  • Date - of first commit of the suite: 2022-10-19
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/minipolish
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/minipolish
  • Galaxy - wrapper version: 0.1.3
  • Conda id: minipolish
  • Conda - version: 0.1.3
  • EDAM operation (no superclasses): - Localised reassembly, Read depth analysis
  • EDAM topic (no superclasses): - Sequence assembly, Sequencing
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 229
  • No. of tool users (all time) (usegalaxy.eu): 229
  • Tool - usage (5 years) (usegalaxy.eu): 32
  • Tool usage (all time) - (usegalaxy.eu): 32
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 229
  • No. of tool users (all time) - all main - servers: 229
  • Tool usage (5 years) - all main servers: - 32
  • Tool usage (all time) - all main servers: 32
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Polishing miniasm assemblies title_md: minipolish - - description_md: '
  • Galaxy tool ids: miniprot, miniprot_index
  • Description: - Align a protein sequence against a genome with affine gap penalty, splicing - and frameshift.
  • bio.tool id: miniprot
  • bio.tool - ids: miniprot
  • biii: nan
  • bio.tool name: - miniprot
  • 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.
  • EDAM operation: Sequence - alignment, Protein sequence analysis
  • EDAM topic: Sequence - sites, features and motifs, Sequence analysis
  • Status: Up-to-date
  • Source: - https://github.com/lh3/miniprot
  • ToolShed categories: Sequence - Analysis
  • ToolShed id: nan
  • Date of first commit - of the suite: 2023-03-23
  • Galaxy wrapper owner: iuc
  • Galaxy - wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot
  • Galaxy - wrapper version: 0.13
  • Conda id: miniprot
  • Conda - version: 0.13
  • EDAM operation (no superclasses): - Sequence alignment, Protein sequence analysis
  • EDAM topic (no superclasses): - Sequence sites, features and motifs, Sequence analysis
  • Available - on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 2
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1244
  • No. of tool - users (all time) (usegalaxy.eu): 1244
  • Tool usage (5 years) - (usegalaxy.eu): 86
  • Tool usage (all time) (usegalaxy.eu): - 86
  • No. of tool users (5 years) (usegalaxy.org): 24
  • No. - of tool users (all time) (usegalaxy.org): 24
  • Tool usage - (5 years) (usegalaxy.org): 15
  • Tool usage (all time) (usegalaxy.org): - 15
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1268
  • No. - of tool users (all time) - all main servers: 1268
  • Tool - usage (5 years) - all main servers: 101
  • Tool usage (all - time) - all main servers: 101
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Align a protein sequence against a genome with affine gap penalty, + splicing and frameshift. title_md: miniprot - - description_md: '
  • Galaxy tool ids: mitos, mitos2
  • Description: - de-novo annotation of metazoan mitochondrial genomes
  • bio.tool - id: mitos
  • bio.tool ids: mitos
  • biii: - nan
  • bio.tool name: MITOS
  • bio.tool description: - De novo metazoan mitochondrial genome annotation.
  • EDAM operation: - Genome annotation
  • EDAM topic: Zoology, Whole genome sequencing
  • Status: - To update
  • Source: http://mitos.bioinf.uni-leipzig.de/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: mitos
  • Date - of first commit of the suite: 2020-02-18
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos
  • Galaxy - wrapper version: 1.1.7
  • Conda id: mitos
  • Conda - version: 2.1.9
  • EDAM operation (no superclasses): - Genome annotation
  • EDAM topic (no superclasses): Zoology, - Whole genome sequencing
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 2
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 191295
  • No. of tool users (all time) (usegalaxy.eu): 191295
  • Tool - usage (5 years) (usegalaxy.eu): 1111
  • Tool usage (all time) - (usegalaxy.eu): 1111
  • No. of tool users (5 years) (usegalaxy.org): - 42265
  • No. of tool users (all time) (usegalaxy.org): 42265
  • Tool - usage (5 years) (usegalaxy.org): 320
  • Tool usage (all time) - (usegalaxy.org): 320
  • No. of tool users (5 years) (usegalaxy.org.au): - 10904
  • No. of tool users (all time) (usegalaxy.org.au): - 10904
  • Tool usage (5 years) (usegalaxy.org.au): 83
  • Tool - usage (all time) (usegalaxy.org.au): 83
  • No. of tool users - (5 years) - all main servers: 244464
  • No. of tool users - (all time) - all main servers: 244464
  • Tool usage (5 years) - - all main servers: 1514
  • Tool usage (all time) - all main - servers: 1514
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: de-novo annotation of metazoan mitochondrial genomes title_md: mitos - - description_md: '
  • Galaxy tool ids: mlst, mlst_list
  • Description: - Scan contig files against PubMLST typing schemes
  • bio.tool id: - mlst
  • bio.tool ids: mlst
  • biii: nan
  • bio.tool - name: MLST
  • bio.tool description: Multi Locus Sequence - Typing from an assembled genome or from a set of reads.
  • EDAM operation: - Multilocus sequence typing
  • EDAM topic: Immunoproteins and - antigens
  • Status: To update
  • Source: - https://github.com/tseemann/mlst
  • ToolShed categories: Sequence - Analysis
  • ToolShed id: mlst
  • Date of first - commit of the suite: 2016-12-12
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst
  • Galaxy - wrapper version: 2.22.0
  • Conda id: mlst
  • Conda - version: 2.23.0
  • EDAM operation (no superclasses): - Multilocus sequence typing
  • EDAM topic (no superclasses): - Immunoproteins and antigens
  • Available on UseGalaxy.org (Main): - 2
  • Available on UseGalaxy.org.au: 2
  • Available - on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 2
  • Tools - available on UseGalaxy.org (Main): 2
  • Tools available on - UseGalaxy.org.au: 2
  • Tools available on UseGalaxy.eu: - 2
  • Tools available on UseGalaxy.fr: 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: 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.no: 2
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 13300
  • No. of tool users (all time) (usegalaxy.eu): 13471
  • Tool - usage (5 years) (usegalaxy.eu): 1480
  • Tool usage (all time) - (usegalaxy.eu): 1501
  • No. of tool users (5 years) (usegalaxy.org): - 6532
  • No. of tool users (all time) (usegalaxy.org): 6532
  • Tool - usage (5 years) (usegalaxy.org): 1167
  • Tool usage (all time) - (usegalaxy.org): 1167
  • No. of tool users (5 years) (usegalaxy.org.au): - 10334
  • No. of tool users (all time) (usegalaxy.org.au): - 11841
  • Tool usage (5 years) (usegalaxy.org.au): 1083
  • Tool - usage (all time) (usegalaxy.org.au): 1300
  • No. of tool users - (5 years) - all main servers: 30166
  • No. of tool users (all - time) - all main servers: 31844
  • Tool usage (5 years) - - all main servers: 3730
  • Tool usage (all time) - all main - servers: 3968
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: Scan contig files against PubMLST typing schemes title_md: mlst - - description_md: '
  • Galaxy tool ids: mob_recon, mob_typer
  • Description: - MOB-suite is a set of software tools for clustering, reconstruction and typing - of plasmids from draft assemblies
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://github.com/phac-nml/mob-suite
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: mob_suite
  • Date - of first commit of the suite: 2018-08-20
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/mob-suite
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite
  • Galaxy - wrapper version: 3.0.3
  • Conda id: mob_suite
  • Conda - version: 3.1.9
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 2
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 2
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: - 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 119024
  • No. of tool - users (all time) (usegalaxy.eu): 119024
  • Tool usage (5 years) - (usegalaxy.eu): 628
  • Tool usage (all time) (usegalaxy.eu): - 628
  • No. of tool users (5 years) (usegalaxy.org): 42
  • No. - of tool users (all time) (usegalaxy.org): 42
  • Tool usage - (5 years) (usegalaxy.org): 2
  • Tool usage (all time) (usegalaxy.org): - 2
  • No. of tool users (5 years) (usegalaxy.org.au): 36310
  • No. - of tool users (all time) (usegalaxy.org.au): 36310
  • Tool - usage (5 years) (usegalaxy.org.au): 191
  • Tool usage (all - time) (usegalaxy.org.au): 191
  • No. of tool users (5 years) - - all main servers: 155376
  • No. of tool users (all time) - - all main servers: 155376
  • Tool usage (5 years) - all main - servers: 821
  • Tool usage (all time) - all main servers: - 821
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: MOB-suite is a set of software tools for clustering, reconstruction + and typing of plasmids from draft assemblies title_md: mob_suite - - description_md: '
  • 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
  • Description: - Mothur wrappers
  • bio.tool id: mothur
  • bio.tool - ids: mothur
  • biii: nan
  • bio.tool name: - mothur
  • bio.tool description: Open-source, platform-independent, - community-supported software for describing and comparing microbial communities
  • EDAM - operation: DNA barcoding, Sequencing quality control, Sequence clustering, - Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic - analysis
  • EDAM topic: Microbial ecology, Taxonomy, Sequence - analysis, Phylogeny
  • Status: To update
  • Source: - https://www.mothur.org
  • ToolShed categories: Metagenomics
  • ToolShed - id: mothur
  • Date of first commit of the suite: 2018-08-03
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur
  • Galaxy - wrapper version: 1.0
  • Conda id: mothur
  • Conda - version: 1.48.0
  • EDAM operation (no superclasses): - DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, - Visualisation, Sequence read processing, Phylogenetic analysis
  • EDAM - topic (no superclasses): Microbial ecology, Taxonomy, Sequence analysis, - Phylogeny
  • Available on UseGalaxy.org (Main): 129
  • Available - on UseGalaxy.org.au: 129
  • Available on UseGalaxy.eu: - 129
  • Available on UseGalaxy.fr: 129
  • Tools - available on UseGalaxy.org (Main): 129
  • Tools available - on UseGalaxy.org.au: 129
  • Tools available on UseGalaxy.eu: - 129
  • Tools available on UseGalaxy.fr: 129
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 129
  • Tools available on Viral - Variant Visualizer (VVV): 0
  • No. of tool users (5 years) - (usegalaxy.eu): 297546
  • No. of tool users (all time) (usegalaxy.eu): - 326056
  • Tool usage (5 years) (usegalaxy.eu): 37506
  • Tool - usage (all time) (usegalaxy.eu): 41763
  • No. of tool users - (5 years) (usegalaxy.org): 565218
  • No. of tool users (all - time) (usegalaxy.org): 682083
  • Tool usage (5 years) (usegalaxy.org): - 72163
  • Tool usage (all time) (usegalaxy.org): 89926
  • No. - of tool users (5 years) (usegalaxy.org.au): 167400
  • No. - of tool users (all time) (usegalaxy.org.au): 182490
  • Tool - usage (5 years) (usegalaxy.org.au): 26963
  • Tool usage (all - time) (usegalaxy.org.au): 28404
  • No. of tool users (5 years) - - all main servers: 1030164
  • No. of tool users (all time) - - all main servers: 1190629
  • Tool usage (5 years) - all - main servers: 136632
  • Tool usage (all time) - all main servers: - 160093
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Mothur wrappers title_md: mothur - - description_md: '
  • Galaxy tool ids: mrbayes
  • Description: - A program for the Bayesian estimation of phylogeny.
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: nan
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: mrbayes
  • Date - of first commit of the suite: 2015-12-04
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: nan
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes
  • Galaxy - wrapper version: 1.0.2
  • Conda id: mrbayes
  • Conda - version: 3.2.7
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
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  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: A program for the Bayesian estimation of phylogeny. title_md: mrbayes - - description_md: '
  • Galaxy tool ids: msconvert
  • Description: - msconvert Convert and/or filter mass spectrometry files (including vendor formats) - using the official Docker container
  • bio.tool id: msconvert
  • bio.tool - ids: msconvert
  • biii: nan
  • bio.tool - name: msConvert
  • 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.
  • EDAM - operation: Filtering, Formatting
  • EDAM topic: Proteomics, - Proteomics experiment
  • Status: To update
  • Source: - http://proteowizard.sourceforge.net/tools.shtml
  • ToolShed categories: - Proteomics
  • ToolShed id: msconvert
  • Date of - first commit of the suite: 2019-02-14
  • Galaxy wrapper owner: - galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
  • Galaxy - wrapper version: 3.0.20287
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): Filtering, - Formatting
  • EDAM topic (no superclasses): Proteomics, Proteomics - experiment
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 20749
  • No. of tool - users (all time) (usegalaxy.eu): 22184
  • Tool usage (5 years) - (usegalaxy.eu): 455
  • Tool usage (all time) (usegalaxy.eu): - 469
  • No. of tool users (5 years) (usegalaxy.org): 1239
  • No. - of tool users (all time) (usegalaxy.org): 1239
  • Tool usage - (5 years) (usegalaxy.org): 71
  • Tool usage (all time) (usegalaxy.org): - 71
  • No. of tool users (5 years) (usegalaxy.org.au): 2666
  • No. - of tool users (all time) (usegalaxy.org.au): 2666
  • Tool - usage (5 years) (usegalaxy.org.au): 53
  • Tool usage (all - time) (usegalaxy.org.au): 53
  • No. of tool users (5 years) - - all main servers: 24654
  • No. of tool users (all time) - - all main servers: 26089
  • Tool usage (5 years) - all main - servers: 579
  • Tool usage (all time) - all main servers: - 593
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: msconvert Convert and/or filter mass spectrometry files (including + vendor formats) using the official Docker container title_md: msconvert - - description_md: '
  • Galaxy tool ids: msstatstmt
  • Description: - MSstatsTMT protein significance analysis in shotgun mass spectrometry-based - proteomic experiments with tandem mass tag (TMT) labeling
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: http://msstats.org/msstatstmt/
  • ToolShed - categories: Proteomics
  • ToolShed id: msstatstmt
  • Date - of first commit of the suite: 2021-02-26
  • Galaxy wrapper - owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt
  • Galaxy - wrapper version: 2.0.0
  • Conda id: bioconductor-msstatstmt
  • Conda - version: 2.10.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
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  • No. of tool - users (all time) (usegalaxy.eu): 795
  • Tool usage (5 years) - (usegalaxy.eu): 104
  • Tool usage (all time) (usegalaxy.eu): - 104
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 461
  • No. - of tool users (all time) (usegalaxy.org.au): 461
  • Tool usage - (5 years) (usegalaxy.org.au): 12
  • Tool usage (all time) - (usegalaxy.org.au): 12
  • No. of tool users (5 years) - all - main servers: 1256
  • No. of tool users (all time) - all main - servers: 1256
  • Tool usage (5 years) - all main servers: - 116
  • Tool usage (all time) - all main servers: 116
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: MSstatsTMT protein significance analysis in shotgun mass spectrometry-based + proteomic experiments with tandem mass tag (TMT) labeling title_md: msstatstmt - - description_md: '
  • Galaxy tool ids: multigsea
  • Description: - GSEA-based pathway enrichment analysis for multi-omics data
  • bio.tool - id: multiGSEA
  • bio.tool ids: multiGSEA
  • biii: - nan
  • bio.tool name: multiGSEA
  • 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.
  • EDAM - operation: Gene-set enrichment analysis, Aggregation, Pathway analysis
  • EDAM - topic: Metabolomics, Molecular interactions, pathways and networks, Proteomics, - Transcriptomics, Small molecules
  • Status: Up-to-date
  • Source: - https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html
  • ToolShed - categories: Transcriptomics, Proteomics, Statistics
  • ToolShed - id: multigsea
  • Date of first commit of the suite: - 2023-06-07
  • Galaxy wrapper owner: iuc
  • Galaxy - wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea
  • Galaxy - wrapper version: 1.12.0
  • Conda id: bioconductor-multigsea
  • Conda - version: 1.12.0
  • EDAM operation (no superclasses): - Gene-set enrichment analysis, Aggregation, Pathway analysis
  • EDAM - topic (no superclasses): Metabolomics, Molecular interactions, pathways - and networks, Proteomics, Transcriptomics, Small molecules
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 106
  • No. of tool - users (all time) (usegalaxy.eu): 106
  • Tool usage (5 years) - (usegalaxy.eu): 25
  • Tool usage (all time) (usegalaxy.eu): - 25
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 106
  • No. - of tool users (all time) - all main servers: 106
  • Tool usage - (5 years) - all main servers: 25
  • Tool usage (all time) - - all main servers: 25
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: GSEA-based pathway enrichment analysis for multi-omics data title_md: multigsea - - description_md: '
  • Galaxy tool ids: multiqc
  • Description: - MultiQC aggregates results from bioinformatics analyses across many samples - into a single report
  • bio.tool id: multiqc
  • bio.tool - ids: multiqc
  • biii: nan
  • bio.tool name: - MultiQC
  • 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.
  • EDAM operation: Validation, Sequencing quality control
  • EDAM - topic: Sequencing, Bioinformatics, Sequence analysis, Genomics
  • Status: - To update
  • Source: http://multiqc.info/
  • ToolShed - categories: Fastq Manipulation, Statistics, Visualization
  • ToolShed - id: multiqc
  • Date of first commit of the suite: 2020-04-28
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc
  • Galaxy - wrapper version: 1.24.1
  • Conda id: multiqc
  • Conda - version: 1.25.1
  • EDAM operation (no superclasses): - Sequencing quality control
  • EDAM topic (no superclasses): - Sequencing, Bioinformatics, Sequence analysis, Genomics
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 182221
  • No. of tool - users (all time) (usegalaxy.eu): 192389
  • Tool usage (5 years) - (usegalaxy.eu): 19343
  • Tool usage (all time) (usegalaxy.eu): - 20494
  • No. of tool users (5 years) (usegalaxy.org): 163961
  • No. - of tool users (all time) (usegalaxy.org): 182413
  • Tool usage - (5 years) (usegalaxy.org): 26449
  • Tool usage (all time) - (usegalaxy.org): 29758
  • No. of tool users (5 years) (usegalaxy.org.au): - 40663
  • No. of tool users (all time) (usegalaxy.org.au): - 41855
  • Tool usage (5 years) (usegalaxy.org.au): 5974
  • Tool - usage (all time) (usegalaxy.org.au): 6157
  • No. of tool users - (5 years) - all main servers: 386845
  • No. of tool users - (all time) - all main servers: 416657
  • Tool usage (5 years) - - all main servers: 51766
  • Tool usage (all time) - all main - servers: 56409
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: MultiQC aggregates results from bioinformatics analyses across + many samples into a single report title_md: multiqc - - description_md: '
  • Galaxy tool ids: mykrobe_predict
  • Description: - Antibiotic resistance predictions
  • bio.tool id: Mykrobe
  • bio.tool - ids: Mykrobe
  • biii: nan
  • bio.tool name: - Mykrobe
  • 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
  • EDAM - operation: Antimicrobial resistance prediction, Variant calling, Genotyping, - Sequence trimming
  • EDAM topic: Whole genome sequencing, - Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics
  • Status: - To update
  • Source: https://github.com/Mykrobe-tools/mykrobe
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: mykrobe
  • Date - of first commit of the suite: 2017-12-18
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe
  • Galaxy - wrapper version: 0.10.0
  • Conda id: mykrobe
  • Conda - version: 0.13.0
  • EDAM operation (no superclasses): - Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming
  • EDAM - topic (no superclasses): Whole genome sequencing, Genotype and phenotype, - Probes and primers, Genetic variation, Metagenomics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Antibiotic resistance predictions title_md: mykrobe - - description_md: '
  • Galaxy tool ids: mykrobe_parseR
  • Description: - RScript to parse the results of mykrobe predictor.
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: https://github.com/phac-nml/mykrobe-parser
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: mykrobe_parser
  • Date - of first commit of the suite: 2018-09-28
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/mykrobe-parser
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser
  • Galaxy - wrapper version: 0.1.4.1
  • Conda id: r-base
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: RScript to parse the results of mykrobe predictor. title_md: mykrobe_parser - - description_md: '
  • Galaxy tool ids: mz_to_sqlite
  • Description: - Creates a SQLite database for proteomics data
  • bio.tool id: - mztosqlite
  • bio.tool ids: mztosqlite
  • biii: - nan
  • bio.tool name: mzToSQLite
  • bio.tool description: - Convert proteomics data files into a SQLite database
  • EDAM operation: - Conversion, Peptide database search
  • EDAM topic: Proteomics, - Biological databases
  • Status: To update
  • Source: - https://github.com/galaxyproteomics/mzToSQLite
  • ToolShed categories: - Proteomics
  • ToolShed id: mz_to_sqlite
  • Date - of first commit of the suite: 2015-06-01
  • Galaxy wrapper - owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite
  • Galaxy - wrapper version: 2.1.1+galaxy0
  • Conda id: mztosqlite
  • Conda - version: 2.1.1
  • EDAM operation (no superclasses): - Conversion, Peptide database search
  • EDAM topic (no superclasses): - Proteomics, Biological databases
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 854
  • No. of tool users (all time) (usegalaxy.eu): 860
  • Tool - usage (5 years) (usegalaxy.eu): 110
  • Tool usage (all time) - (usegalaxy.eu): 111
  • No. of tool users (5 years) (usegalaxy.org): - 79
  • No. of tool users (all time) (usegalaxy.org): 79
  • Tool - usage (5 years) (usegalaxy.org): 15
  • Tool usage (all time) - (usegalaxy.org): 15
  • No. of tool users (5 years) (usegalaxy.org.au): - 274
  • No. of tool users (all time) (usegalaxy.org.au): 274
  • Tool - usage (5 years) (usegalaxy.org.au): 13
  • Tool usage (all - time) (usegalaxy.org.au): 13
  • No. of tool users (5 years) - - all main servers: 1207
  • No. of tool users (all time) - - all main servers: 1213
  • Tool usage (5 years) - all main - servers: 138
  • Tool usage (all time) - all main servers: - 139
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Creates a SQLite database for proteomics data title_md: mz_to_sqlite - - description_md: '
  • Galaxy tool ids: nanocompore_db, nanocompore_sampcomp
  • 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.
  • bio.tool id: Nanocompore
  • bio.tool - ids: Nanocompore
  • biii: nan
  • bio.tool - name: Nanocompore
  • 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
  • EDAM - operation: Post-translation modification site prediction, 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
  • Status: To update
  • Source: - https://nanocompore.rna.rocks/
  • ToolShed categories: Sequence - Analysis
  • ToolShed id: nanocompore
  • Date of - first commit of the suite: 2020-05-01
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore
  • Galaxy - wrapper version: 1.0.0rc3.post2
  • Conda id: nanocompore
  • Conda - version: 1.0.4
  • EDAM operation (no superclasses): - PolyA signal detection, Genotyping, k-mer counting
  • EDAM topic - (no superclasses): Functional, regulatory and non-coding RNA, RNA-Seq, - Gene transcripts, Transcriptomics, Transcription factors and regulatory sites
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 839
  • No. of tool - users (all time) (usegalaxy.eu): 839
  • Tool usage (5 years) - (usegalaxy.eu): 12
  • Tool usage (all time) (usegalaxy.eu): - 12
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 269
  • No. - of tool users (all time) (usegalaxy.org.au): 269
  • Tool usage - (5 years) (usegalaxy.org.au): 5
  • Tool usage (all time) (usegalaxy.org.au): - 5
  • No. of tool users (5 years) - all main servers: 1108
  • No. - of tool users (all time) - all main servers: 1108
  • Tool - usage (5 years) - all main servers: 17
  • Tool usage (all - time) - all main servers: 17
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: 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. title_md: nanocompore - - description_md: '
  • Galaxy tool ids: nanoplot
  • Description: - Plotting tool for long read sequencing data and alignments
  • bio.tool - id: nanoplot
  • bio.tool ids: nanoplot
  • biii: - nan
  • bio.tool name: NanoPlot
  • 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
  • EDAM - operation: Scatter plot plotting, Box-Whisker plot plotting
  • EDAM - topic: Genomics
  • Status: Up-to-date
  • Source: - https://github.com/wdecoster/NanoPlot
  • ToolShed categories: - Visualization
  • ToolShed id: nanoplot
  • Date - of first commit of the suite: 2018-09-28
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot
  • Galaxy - wrapper version: 1.43.0
  • Conda id: nanoplot
  • Conda - version: 1.43.0
  • EDAM operation (no superclasses): - Scatter plot plotting, Box-Whisker plot plotting
  • EDAM topic (no - superclasses): Genomics
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 99052
  • No. of tool users (all time) (usegalaxy.eu): 100009
  • Tool - usage (5 years) (usegalaxy.eu): 5671
  • Tool usage (all time) - (usegalaxy.eu): 5755
  • No. of tool users (5 years) (usegalaxy.org): - 40386
  • No. of tool users (all time) (usegalaxy.org): 40386
  • Tool - usage (5 years) (usegalaxy.org): 3371
  • Tool usage (all time) - (usegalaxy.org): 3371
  • No. of tool users (5 years) (usegalaxy.org.au): - 17919
  • No. of tool users (all time) (usegalaxy.org.au): - 17919
  • Tool usage (5 years) (usegalaxy.org.au): 2188
  • Tool - usage (all time) (usegalaxy.org.au): 2188
  • No. of tool users - (5 years) - all main servers: 157357
  • No. of tool users - (all time) - all main servers: 158314
  • Tool usage (5 years) - - all main servers: 11230
  • Tool usage (all time) - all main - servers: 11314
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: Plotting tool for long read sequencing data and alignments title_md: nanoplot - - description_md: '
  • Galaxy tool ids: nanopolishcomp_eventaligncollapse, - nanopolishcomp_freqmethcalculate
  • 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.
  • bio.tool - id: nanopolishcomp
  • bio.tool ids: nanopolishcomp
  • biii: - nan
  • bio.tool name: NanopolishComp
  • bio.tool - description: NanopolishComp is a Python3 package for downstream analyses - of Nanopolish output files.It is a companion package for Nanopolish.
  • EDAM - operation: Methylation analysis, Collapsing methods
  • EDAM - topic: Sequence analysis, Sequencing, Genetic variation
  • Status: - To update
  • Source: https://a-slide.github.io/NanopolishComp
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: nanopolishcomp
  • Date - of first commit of the suite: 2020-04-27
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp
  • Galaxy - wrapper version: 0.6.11
  • Conda id: nanopolishcomp
  • Conda - version: 0.6.12
  • EDAM operation (no superclasses): - Methylation analysis, Collapsing methods
  • EDAM topic (no superclasses): - Sequence analysis, Sequencing, Genetic variation
  • Available on - UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1091
  • No. of tool - users (all time) (usegalaxy.eu): 1091
  • Tool usage (5 years) - (usegalaxy.eu): 44
  • Tool usage (all time) (usegalaxy.eu): - 44
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1091
  • No. - of tool users (all time) - all main servers: 1091
  • Tool - usage (5 years) - all main servers: 44
  • Tool usage (all - time) - all main servers: 44
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: 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. title_md: nanopolishcomp - - description_md: '
  • Galaxy tool ids: blastxml_to_tabular, get_species_taxids, - ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, - ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, - ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, - ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, - ncbi_tblastx_wrapper
  • Description: NCBI BLAST+
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: https://blast.ncbi.nlm.nih.gov/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: ncbi_blast_plus
  • Date - of first commit of the suite: 2020-09-08
  • Galaxy wrapper - owner: devteam
  • Galaxy wrapper source: https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus
  • Galaxy - wrapper parsed folder: https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus
  • Galaxy - wrapper version: 2.14.1
  • Conda id: python
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 16
  • Available on UseGalaxy.org.au: 16
  • Available - on UseGalaxy.eu: 16
  • Available on UseGalaxy.fr: 16
  • Tools - available on UseGalaxy.org (Main): 16
  • Tools available on - UseGalaxy.org.au: 16
  • Tools available on UseGalaxy.eu: - 16
  • Tools available on UseGalaxy.fr: 16
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 16
  • Tools available on Galaxy@Pasteur: - 15
  • Tools available on GalaxyTrakr: 16
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 16
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 16
  • Tools - available on PhagePromotor: 15
  • Tools available on UseGalaxy.be: - 16
  • Tools available on UseGalaxy.cz: 16
  • Tools - available on UseGalaxy.no: 15
  • Tools available on Viral - Variant Visualizer (VVV): 0
  • No. of tool users (5 years) - (usegalaxy.eu): 391141
  • No. of tool users (all time) (usegalaxy.eu): - 443752
  • Tool usage (5 years) (usegalaxy.eu): 9760
  • Tool - usage (all time) (usegalaxy.eu): 10546
  • No. of tool users - (5 years) (usegalaxy.org): 306361
  • No. of tool users (all - time) (usegalaxy.org): 350178
  • Tool usage (5 years) (usegalaxy.org): - 11767
  • Tool usage (all time) (usegalaxy.org): 13684
  • No. - of tool users (5 years) (usegalaxy.org.au): 227235
  • No. - of tool users (all time) (usegalaxy.org.au): 244814
  • Tool - usage (5 years) (usegalaxy.org.au): 3192
  • Tool usage (all - time) (usegalaxy.org.au): 3617
  • No. of tool users (5 years) - - all main servers: 924737
  • No. of tool users (all time) - - all main servers: 1038744
  • Tool usage (5 years) - all - main servers: 24719
  • Tool usage (all time) - all main servers: - 27847
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: NCBI BLAST+ title_md: ncbi_blast_plus - - description_md: '
  • Galaxy tool ids: ncbi_fcs_gx
  • Description: - FCS-GX detects contamination from foreign organisms in genome sequences using - the genome cross-species aligner (GX).
  • bio.tool id: ncbi_fcs
  • bio.tool - ids: ncbi_fcs
  • biii: nan
  • bio.tool name: - NCBI fcs
  • 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.
  • EDAM operation: - Sequence assembly validation, Sequence trimming, Sequence contamination filtering
  • EDAM - topic: Sequence analysis, Sequence assembly
  • Status: - Up-to-date
  • Source: https://github.com/ncbi/fcs-gx
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: ncbi_fcs_gx
  • Date - of first commit of the suite: 2023-11-14
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx
  • Galaxy - wrapper version: 0.5.4
  • Conda id: ncbi-fcs-gx
  • Conda - version: 0.5.4
  • EDAM operation (no superclasses): - Sequence assembly validation, Sequence trimming, Sequence contamination filtering
  • EDAM - topic (no superclasses): Sequence analysis, Sequence assembly
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 125
  • No. of tool - users (all time) (usegalaxy.eu): 125
  • Tool usage (5 years) - (usegalaxy.eu): 26
  • Tool usage (all time) (usegalaxy.eu): - 26
  • No. of tool users (5 years) (usegalaxy.org): 2489
  • No. - of tool users (all time) (usegalaxy.org): 2489
  • Tool usage - (5 years) (usegalaxy.org): 139
  • Tool usage (all time) (usegalaxy.org): - 139
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 2614
  • No. - of tool users (all time) - all main servers: 2614
  • Tool - usage (5 years) - all main servers: 165
  • Tool usage (all - time) - all main servers: 165
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: FCS-GX detects contamination from foreign organisms in genome + sequences using the genome cross-species aligner (GX). title_md: ncbi_fcs_gx - - description_md: '
  • Galaxy tool ids: newick_display
  • Description: - Perform operations on Newick trees
  • bio.tool id: newick_utilities
  • bio.tool - ids: newick_utilities
  • biii: nan
  • bio.tool - name: Newick Utilities
  • 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.
  • EDAM operation: Phylogenetic tree generation, Phylogenetic - tree analysis, Phylogenetic tree reconstruction
  • EDAM topic: - Phylogeny, Genomics, Computer science
  • Status: To update
  • Source: - http://cegg.unige.ch/newick_utils
  • ToolShed categories: - Visualization, Metagenomics
  • ToolShed id: newick_utils
  • Date - of first commit of the suite: 2018-10-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/tjunier/newick_utils
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils
  • Galaxy - wrapper version: 1.6+galaxy1
  • Conda id: newick_utils
  • Conda - version: 1.6
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): Phylogeny, Genomics, Computer science
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 33637
  • No. of tool - users (all time) (usegalaxy.eu): 34195
  • Tool usage (5 years) - (usegalaxy.eu): 1113
  • Tool usage (all time) (usegalaxy.eu): - 1172
  • No. of tool users (5 years) (usegalaxy.org): 16257
  • No. - of tool users (all time) (usegalaxy.org): 16257
  • Tool usage - (5 years) (usegalaxy.org): 1816
  • Tool usage (all time) (usegalaxy.org): - 1816
  • No. of tool users (5 years) (usegalaxy.org.au): 7582
  • No. - of tool users (all time) (usegalaxy.org.au): 7582
  • Tool - usage (5 years) (usegalaxy.org.au): 899
  • Tool usage (all - time) (usegalaxy.org.au): 899
  • No. of tool users (5 years) - - all main servers: 57476
  • No. of tool users (all time) - - all main servers: 58034
  • Tool usage (5 years) - all main - servers: 3828
  • Tool usage (all time) - all main servers: - 3887
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Perform operations on Newick trees title_md: newick_utils - - description_md: '
  • Galaxy tool ids: nextalign, nextclade
  • Description: - Identify differences between your sequences and a reference sequence used by - Nextstrain
  • bio.tool id: nextclade
  • bio.tool - ids: nextclade
  • biii: nan
  • bio.tool - name: Nextclade
  • bio.tool description: Nextclade - is an open-source project for viral genome alignment, mutation calling, clade - assignment, quality checks and phylogenetic placement.
  • EDAM operation: - Methylation analysis, Variant calling
  • EDAM topic: Genomics, - Sequence analysis, Cladistics
  • Status: To update
  • Source: - https://github.com/nextstrain/nextclade
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: nan
  • Date of - first commit of the suite: 2021-04-26
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade
  • Galaxy - wrapper version: 2.7.0
  • Conda id: nextalign
  • Conda - version: 2.14.0
  • EDAM operation (no superclasses): - Methylation analysis, Variant calling
  • EDAM topic (no superclasses): - Genomics, Cladistics
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 2
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 2
  • Tools available on UseGalaxy.fr: 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: 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 4411
  • No. of tool users (all time) (usegalaxy.eu): 4411
  • Tool - usage (5 years) (usegalaxy.eu): 396
  • Tool usage (all time) - (usegalaxy.eu): 396
  • No. of tool users (5 years) (usegalaxy.org): - 9708
  • No. of tool users (all time) (usegalaxy.org): 9708
  • Tool - usage (5 years) (usegalaxy.org): 279
  • Tool usage (all time) - (usegalaxy.org): 279
  • No. of tool users (5 years) (usegalaxy.org.au): - 2099
  • No. of tool users (all time) (usegalaxy.org.au): 2099
  • Tool - usage (5 years) (usegalaxy.org.au): 212
  • Tool usage (all - time) (usegalaxy.org.au): 212
  • No. of tool users (5 years) - - all main servers: 16218
  • No. of tool users (all time) - - all main servers: 16218
  • Tool usage (5 years) - all main - servers: 887
  • Tool usage (all time) - all main servers: - 887
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Identify differences between your sequences and a reference sequence + used by Nextstrain title_md: nextclade - - description_md: '
  • Galaxy tool ids: nextdenovo
  • Description: - String graph-based de novo assembler for long reads
  • bio.tool id: - nextdenovo
  • bio.tool ids: nextdenovo
  • biii: - nan
  • bio.tool name: NextDenovo
  • bio.tool description: - NextDenovo 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.
  • EDAM operation: De-novo assembly, Genome - assembly
  • EDAM topic: Sequencing, Sequence assembly
  • Status: - To update
  • Source: https://github.com/Nextomics/NextDenovo
  • ToolShed - categories: Assembly
  • ToolShed id: nextdenovo
  • Date - of first commit of the suite: 2023-02-09
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo
  • Galaxy - wrapper version: 2.5.0
  • Conda id: nextdenovo
  • Conda - version: 2.5.2
  • EDAM operation (no superclasses): - De-novo assembly, Genome assembly
  • EDAM topic (no superclasses): - Sequencing, Sequence assembly
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 391
  • No. of tool users (all time) (usegalaxy.eu): 391
  • Tool - usage (5 years) (usegalaxy.eu): 158
  • Tool usage (all time) - (usegalaxy.eu): 158
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 391
  • No. of tool users (all time) - all main - servers: 391
  • Tool usage (5 years) - all main servers: - 158
  • Tool usage (all time) - all main servers: 158
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: String graph-based de novo assembler for long reads title_md: nextdenovo - - description_md: '
  • Galaxy tool ids: nonpareil
  • Description: - Estimate average coverage in metagenomic datasets
  • bio.tool id: - nonpareil
  • bio.tool ids: nonpareil
  • biii: - nan
  • bio.tool name: nonpareil
  • bio.tool description: - Estimate metagenomic coverage and sequence diversity
  • EDAM operation: - Operation
  • EDAM topic: nan
  • Status: - To update
  • Source: http://nonpareil.readthedocs.io
  • ToolShed - categories: Metagenomics
  • ToolShed id: nonpareil
  • Date - of first commit of the suite: 2017-11-03
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil
  • Galaxy - wrapper version: 3.1.1
  • Conda id: nonpareil
  • Conda - version: 3.5.5
  • EDAM operation (no superclasses): - Operation
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 107
  • No. of tool - users (all time) (usegalaxy.eu): 143
  • Tool usage (5 years) - (usegalaxy.eu): 13
  • Tool usage (all time) (usegalaxy.eu): - 15
  • No. of tool users (5 years) (usegalaxy.org): 148
  • No. - of tool users (all time) (usegalaxy.org): 148
  • Tool usage - (5 years) (usegalaxy.org): 20
  • Tool usage (all time) (usegalaxy.org): - 20
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 255
  • No. - of tool users (all time) - all main servers: 291
  • Tool usage - (5 years) - all main servers: 33
  • Tool usage (all time) - - all main servers: 35
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Estimate average coverage in metagenomic datasets title_md: nonpareil - - description_md: '
  • Galaxy tool ids: Nucleosome
  • Description: - Prediction of Nucleosomes Positions on the Genome
  • bio.tool id: - nucleosome_prediction
  • bio.tool ids: nucleosome_prediction
  • biii: - nan
  • bio.tool name: nucleosome_prediction
  • bio.tool - description: Prediction of Nucleosomes Positions on the Genome
  • EDAM - operation: Prediction and recognition, Nucleosome position prediction, - Sequence analysis
  • EDAM topic: Structural genomics, Nucleic - acid sites, features and motifs
  • Status: Up-to-date
  • Source: - https://genie.weizmann.ac.il/software/nucleo_exe.html
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: nucleosome_prediction
  • Date - of first commit of the suite: 2016-09-27
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction
  • Galaxy - wrapper version: 3.0
  • Conda id: nucleosome_prediction
  • Conda - version: 3.0
  • EDAM operation (no superclasses): Prediction - and recognition, Nucleosome position prediction, Sequence analysis
  • EDAM - topic (no superclasses): Structural genomics, Nucleic acid sites, features - and motifs
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 118
  • No. of tool - users (all time) (usegalaxy.eu): 863
  • Tool usage (5 years) - (usegalaxy.eu): 19
  • Tool usage (all time) (usegalaxy.eu): - 26
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 118
  • No. - of tool users (all time) - all main servers: 863
  • Tool usage - (5 years) - all main servers: 19
  • Tool usage (all time) - - all main servers: 26
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Prediction of Nucleosomes Positions on the Genome title_md: nucleosome_prediction - - description_md: '
  • Galaxy tool ids: nugen_nudup
  • Description: - Marks/removes PCR introduced duplicate molecules based on the molecular tagging - technology used in NuGEN products.
  • bio.tool id: nudup
  • bio.tool - ids: nudup
  • biii: nan
  • bio.tool name: - NuDup
  • bio.tool description: Marks/removes duplicate molecules - based on the molecular tagging technology used in Tecan products.
  • EDAM - operation: Duplication detection
  • EDAM topic: Sequencing
  • Status: - Up-to-date
  • Source: https://github.com/tecangenomics/nudup
  • ToolShed - categories: SAM, Metagenomics, Sequence Analysis, Transcriptomics
  • ToolShed - id: nugen_nudup
  • Date of first commit of the suite: - 2016-11-18
  • Galaxy wrapper owner: iuc
  • Galaxy - wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup
  • Galaxy - wrapper version: 2.3.3
  • Conda id: nudup
  • Conda - version: 2.3.3
  • EDAM operation (no superclasses): - Duplication detection
  • EDAM topic (no superclasses): Sequencing
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Marks/removes PCR introduced duplicate molecules based on the + molecular tagging technology used in NuGEN products. title_md: nugen_nudup - - description_md: '
  • Galaxy tool ids: obisindicators, obis_data
  • Description: - Compute biodiveristy indicators for marine data from obis
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: https://github.com/Marie59/obisindicators
  • ToolShed - categories: Ecology
  • ToolShed id: nan
  • Date - of first commit of the suite: 2022-11-04
  • Galaxy wrapper - owner: ecology
  • Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators
  • Galaxy - wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators
  • Galaxy - wrapper version: 0.0.2
  • Conda id: r-base
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 2
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 352
  • No. of tool users (all time) (usegalaxy.eu): 352
  • Tool - usage (5 years) (usegalaxy.eu): 42
  • Tool usage (all time) - (usegalaxy.eu): 42
  • No. of tool users (5 years) (usegalaxy.org): - 8
  • No. of tool users (all time) (usegalaxy.org): 8
  • Tool - usage (5 years) (usegalaxy.org): 6
  • Tool usage (all time) - (usegalaxy.org): 6
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 360
  • No. of tool users (all time) - all main - servers: 360
  • Tool usage (5 years) - all main servers: - 48
  • Tool usage (all time) - all main servers: 48
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Compute biodiveristy indicators for marine data from obis title_md: obisindicators - - description_md: '
  • Galaxy tool ids: obi_illumina_pairend, obi_ngsfilter, - obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, - obi_uniq
  • Description: OBITools is a set of programs developed - to simplify the manipulation of sequence files
  • bio.tool id: - obitools
  • bio.tool ids: obitools
  • biii: - nan
  • bio.tool name: OBITools
  • 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.
  • EDAM - operation: Sequence analysis, Sequence analysis
  • EDAM topic: - Sequence analysis, DNA, Sequencing
  • Status: Up-to-date
  • Source: - http://metabarcoding.org/obitools
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: obitools
  • Date - of first commit of the suite: 2017-03-23
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools
  • Galaxy - wrapper version: 1.2.13
  • Conda id: obitools
  • Conda - version: 1.2.13
  • EDAM operation (no superclasses): - Sequence analysis, Sequence analysis
  • EDAM topic (no superclasses): - Sequence analysis, DNA, Sequencing
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 10
  • Available - on UseGalaxy.eu: 10
  • Available on UseGalaxy.fr: 10
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 10
  • Tools available on UseGalaxy.eu: - 10
  • Tools available on UseGalaxy.fr: 10
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - 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.no: 10
  • Tools available on Viral - Variant Visualizer (VVV): 0
  • No. of tool users (5 years) - (usegalaxy.eu): 37598
  • No. of tool users (all time) (usegalaxy.eu): - 37598
  • Tool usage (5 years) (usegalaxy.eu): 1277
  • Tool - usage (all time) (usegalaxy.eu): 1277
  • No. of tool users - (5 years) (usegalaxy.org): 0
  • No. of tool users (all time) - (usegalaxy.org): 0
  • Tool usage (5 years) (usegalaxy.org): - 0
  • Tool usage (all time) (usegalaxy.org): 0
  • No. - of tool users (5 years) (usegalaxy.org.au): 3862
  • No. of - tool users (all time) (usegalaxy.org.au): 3862
  • Tool usage - (5 years) (usegalaxy.org.au): 280
  • Tool usage (all time) - (usegalaxy.org.au): 280
  • No. of tool users (5 years) - all - main servers: 41460
  • No. of tool users (all time) - all - main servers: 41460
  • Tool usage (5 years) - all main servers: - 1557
  • Tool usage (all time) - all main servers: 1557
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: OBITools is a set of programs developed to simplify the manipulation + of sequence files title_md: obitools - - description_md: '
  • Galaxy tool ids: omark
  • Description: - Proteome quality assessment software
  • bio.tool id: omark
  • bio.tool - ids: omark
  • biii: nan
  • bio.tool name: - OMArk
  • bio.tool description: Proteome quality assessment - software
  • EDAM operation: Sequence assembly validation, - Differential protein expression profiling
  • EDAM topic: Proteomics, - Sequence analysis, Statistics and probability
  • Status: To - update
  • Source: https://github.com/DessimozLab/OMArk
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: omark
  • Date - of first commit of the suite: 2023-11-15
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark
  • Galaxy - wrapper version: 0.3.0
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): Sequence - assembly validation, Differential protein expression profiling
  • EDAM - topic (no superclasses): Proteomics, Sequence analysis, Statistics and - probability
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 158
  • No. of tool - users (all time) (usegalaxy.eu): 158
  • Tool usage (5 years) - (usegalaxy.eu): 12
  • Tool usage (all time) (usegalaxy.eu): - 12
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 158
  • No. - of tool users (all time) - all main servers: 158
  • Tool usage - (5 years) - all main servers: 12
  • Tool usage (all time) - - all main servers: 12
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Proteome quality assessment software title_md: omark - - description_md: '
  • Galaxy tool ids: orfipy
  • Description: - Galaxy wrapper for ORFIPY
  • bio.tool id: orfipy
  • bio.tool - ids: orfipy
  • biii: nan
  • bio.tool name: - orfipy
  • 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.
  • EDAM - operation: Coding region prediction, Database search, Transcriptome assembly, - De-novo assembly
  • EDAM topic: Computer science, RNA-Seq, - Transcriptomics, Small molecules
  • Status: Up-to-date
  • Source: - https://github.com/urmi-21/orfipy
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: orfipy
  • Date - of first commit of the suite: 2022-04-07
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy
  • Galaxy - wrapper version: 0.0.4
  • Conda id: orfipy
  • Conda - version: 0.0.4
  • EDAM operation (no superclasses): - Coding region prediction, Database search, Transcriptome assembly, De-novo assembly
  • EDAM - topic (no superclasses): Computer science, RNA-Seq, Transcriptomics, - Small molecules
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 897
  • No. of tool - users (all time) (usegalaxy.eu): 897
  • Tool usage (5 years) - (usegalaxy.eu): 99
  • Tool usage (all time) (usegalaxy.eu): - 99
  • No. of tool users (5 years) (usegalaxy.org): 1792
  • No. - of tool users (all time) (usegalaxy.org): 1792
  • Tool usage - (5 years) (usegalaxy.org): 239
  • Tool usage (all time) (usegalaxy.org): - 239
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 2689
  • No. - of tool users (all time) - all main servers: 2689
  • Tool - usage (5 years) - all main servers: 338
  • Tool usage (all - time) - all main servers: 338
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Galaxy wrapper for ORFIPY title_md: orfipy - - description_md: '
  • Galaxy tool ids: orthofinder_onlygroups
  • Description: - Accurate inference of orthologous gene groups made easy
  • bio.tool - id: OrthoFinder
  • bio.tool ids: OrthoFinder
  • biii: - nan
  • bio.tool name: OrthoFinder
  • 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.
  • EDAM - operation: Genome comparison, Phylogenetic tree generation (from molecular - sequences), Phylogenetic tree analysis, Genome alignment
  • EDAM - topic: Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, - Sequence analysis
  • Status: To update
  • Source: - https://github.com/davidemms/OrthoFinder
  • ToolShed categories: - Phylogenetics, Sequence Analysis
  • ToolShed id: orthofinder
  • Date - of first commit of the suite: 2017-08-30
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder
  • Galaxy - wrapper version: 2.5.5
  • Conda id: orthofinder
  • Conda - version: 3.0.1b1
  • EDAM operation (no superclasses): - Genome comparison, Genome alignment
  • EDAM topic (no superclasses): - Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 2018
  • No. of tool - users (all time) (usegalaxy.eu): 2018
  • Tool usage (5 years) - (usegalaxy.eu): 419
  • Tool usage (all time) (usegalaxy.eu): - 419
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 438
  • No. - of tool users (all time) (usegalaxy.org.au): 438
  • Tool usage - (5 years) (usegalaxy.org.au): 58
  • Tool usage (all time) - (usegalaxy.org.au): 58
  • No. of tool users (5 years) - all - main servers: 2456
  • No. of tool users (all time) - all main - servers: 2456
  • Tool usage (5 years) - all main servers: - 477
  • Tool usage (all time) - all main servers: 477
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Accurate inference of orthologous gene groups made easy title_md: orthofinder - - description_md: '
  • Galaxy tool ids: fasta_cli, ident_params, - peptide_shaker, search_gui
  • Description: PeptideShaker and - SearchGUI
  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool - description: nan
  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - http://compomics.github.io
  • ToolShed categories: Proteomics
  • ToolShed - id: peptideshaker
  • Date of first commit of the suite: - 2021-04-02
  • Galaxy wrapper owner: galaxyp
  • Galaxy - wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker
  • Galaxy - wrapper version: nan
  • Conda id: searchgui
  • Conda - version: 4.3.11
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 4
  • Available on UseGalaxy.org.au: - 4
  • Available on UseGalaxy.eu: 4
  • Available - on UseGalaxy.fr: 4
  • Tools available on UseGalaxy.org (Main): - 4
  • Tools available on UseGalaxy.org.au: 4
  • Tools - available on UseGalaxy.eu: 4
  • Tools available on UseGalaxy.fr: - 4
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools 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: 4
  • Tools available on UseGalaxy.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 11986
  • No. of tool - users (all time) (usegalaxy.eu): 17898
  • Tool usage (5 years) - (usegalaxy.eu): 1046
  • Tool usage (all time) (usegalaxy.eu): - 1153
  • No. of tool users (5 years) (usegalaxy.org): 1314
  • No. - of tool users (all time) (usegalaxy.org): 1314
  • Tool usage - (5 years) (usegalaxy.org): 389
  • Tool usage (all time) (usegalaxy.org): - 389
  • No. of tool users (5 years) (usegalaxy.org.au): 3034
  • No. - of tool users (all time) (usegalaxy.org.au): 3034
  • Tool - usage (5 years) (usegalaxy.org.au): 118
  • Tool usage (all - time) (usegalaxy.org.au): 118
  • No. of tool users (5 years) - - all main servers: 16334
  • No. of tool users (all time) - - all main servers: 22246
  • Tool usage (5 years) - all main - servers: 1553
  • Tool usage (all time) - all main servers: - 1660
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: PeptideShaker and SearchGUI title_md: peptideshaker - - description_md: '
  • Galaxy tool ids: pfamscan
  • Description: - Search a FASTA sequence against a library of Pfam HMM.
  • bio.tool - id: pfamscan
  • bio.tool ids: pfamscan
  • biii: - nan
  • bio.tool name: PfamScan
  • bio.tool description: - This tool is used to search a FASTA sequence against a library of Pfam HMM.
  • EDAM - operation: Protein sequence analysis
  • EDAM topic: - Sequence analysis
  • Status: Up-to-date
  • Source: - http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: pfamscan
  • Date - of first commit of the suite: 2023-02-02
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan
  • Galaxy - wrapper version: 1.6
  • Conda id: pfam_scan
  • Conda - version: 1.6
  • EDAM operation (no superclasses): Protein - sequence analysis
  • EDAM topic (no superclasses): Sequence - analysis
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 773
  • No. of tool - users (all time) (usegalaxy.eu): 773
  • Tool usage (5 years) - (usegalaxy.eu): 60
  • Tool usage (all time) (usegalaxy.eu): - 60
  • No. of tool users (5 years) (usegalaxy.org): 495
  • No. - of tool users (all time) (usegalaxy.org): 495
  • Tool usage - (5 years) (usegalaxy.org): 72
  • Tool usage (all time) (usegalaxy.org): - 72
  • No. of tool users (5 years) (usegalaxy.org.au): 246
  • No. - of tool users (all time) (usegalaxy.org.au): 246
  • Tool usage - (5 years) (usegalaxy.org.au): 17
  • Tool usage (all time) - (usegalaxy.org.au): 17
  • No. of tool users (5 years) - all - main servers: 1514
  • No. of tool users (all time) - all main - servers: 1514
  • Tool usage (5 years) - all main servers: - 149
  • Tool usage (all time) - all main servers: 149
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Search a FASTA sequence against a library of Pfam HMM. title_md: pfamscan - - description_md: "
  • Galaxy tool ids: pharokka
  • Description:\ - \ rapid standardised annotation tool for bacteriophage genomes and metagenomes
  • bio.tool\ - \ id: pharokka
  • bio.tool ids: pharokka
  • biii:\ - \ nan
  • bio.tool name: Pharokka
  • bio.tool description:\ - \ Pharokka is a rapid standardised annotation tool for bacteriophage genomes\ - \ and metagenomes.
  • EDAM operation: 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
  • Status: To\ - \ update
  • Source: https://github.com/gbouras13/pharokka
  • ToolShed\ - \ categories: Genome annotation
  • ToolShed id: pharokka
  • Date\ - \ of first commit of the suite: 2023-02-14
  • Galaxy wrapper\ - \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
  • Galaxy\ - \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
  • Galaxy\ - \ wrapper version: 1.3.2
  • Conda id: \n \ - \ pharokka\n
  • Conda version: nan
  • EDAM\ - \ operation (no superclasses): Genome annotation, Antimicrobial resistance\ - \ prediction, tRNA gene prediction, Formatting, Sequence assembly
  • EDAM\ - \ topic (no superclasses): Metagenomics, Sequence sites, features and\ - \ motifs, Workflows, Functional, regulatory and non-coding RNA
  • Available\ - \ on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au:\ - \ 1
  • Available on UseGalaxy.eu: 1
  • Available\ - \ on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main):\ - \ 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools\ - \ available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr:\ - \ 0
  • Tools available on APOSTL: 0
  • Tools available\ - \ on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools\ - \ available on ChemFlow: 0
  • Tools available on Coloc-stats:\ - \ 0
  • Tools available on CropGalaxy: 0
  • Tools\ - \ available 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.no:\ - \ 0
  • Tools available on Viral Variant Visualizer (VVV):\ - \ 0
  • No. of tool users (5 years) (usegalaxy.eu): 5462
  • No.\ - \ of tool users (all time) (usegalaxy.eu): 5462
  • Tool usage\ - \ (5 years) (usegalaxy.eu): 334
  • Tool usage (all time) (usegalaxy.eu):\ - \ 334
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No.\ - \ of tool users (all time) (usegalaxy.org): 0
  • Tool usage\ - \ (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org):\ - \ 0
  • No. of tool users (5 years) (usegalaxy.org.au): 309
  • No.\ - \ of tool users (all time) (usegalaxy.org.au): 309
  • Tool\ - \ usage (5 years) (usegalaxy.org.au): 52
  • Tool usage (all\ - \ time) (usegalaxy.org.au): 52
  • No. of tool users (5 years)\ - \ - all main servers: 5771
  • No. of tool users (all time)\ - \ - all main servers: 5771
  • Tool usage (5 years) - all main\ - \ servers: 386
  • Tool usage (all time) - all main servers:\ - \ 386
  • Reviewed: True
  • To keep: True
  • Deprecated:\ - \ False
" + - description_md: rapid standardised annotation tool for bacteriophage genomes and + metagenomes title_md: pharokka - - description_md: '
  • Galaxy tool ids: phyloseq_from_biom, phyloseq_from_dada2, - phyloseq_plot_ordination, phyloseq_plot_richness
  • Description: - Handling and analysis of high-throughput microbiome census data
  • bio.tool - id: phyloseq
  • bio.tool ids: phyloseq
  • biii: - nan
  • bio.tool name: phyloseq
  • bio.tool description: - Provides a set of classes and tools to facilitate the import, storage, analysis, - and graphical display of microbiome census data.
  • EDAM operation: - Deposition, Analysis, Visualisation
  • EDAM topic: Microbiology, - Sequence analysis, Metagenomics
  • Status: Up-to-date
  • Source: - https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html
  • ToolShed - categories: Metagenomics
  • ToolShed id: phyloseq
  • Date - of first commit of the suite: 2022-03-03
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq
  • Galaxy - wrapper version: 1.46.0
  • Conda id: bioconductor-phyloseq
  • Conda - version: 1.46.0
  • EDAM operation (no superclasses): - Deposition, Analysis, Visualisation
  • EDAM topic (no superclasses): - Microbiology, Sequence analysis, Metagenomics
  • Available on UseGalaxy.org - (Main): 4
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 4
  • Available on UseGalaxy.fr: 4
  • Tools - available on UseGalaxy.org (Main): 4
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 4
  • Tools available on UseGalaxy.fr: 4
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1199
  • No. of tool users (all time) (usegalaxy.eu): 1199
  • Tool - usage (5 years) (usegalaxy.eu): 193
  • Tool usage (all time) - (usegalaxy.eu): 193
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 6
  • No. of tool users (all time) (usegalaxy.org.au): 6
  • Tool - usage (5 years) (usegalaxy.org.au): 1
  • Tool usage (all time) - (usegalaxy.org.au): 1
  • No. of tool users (5 years) - all - main servers: 1205
  • No. of tool users (all time) - all main - servers: 1205
  • Tool usage (5 years) - all main servers: - 194
  • Tool usage (all time) - all main servers: 194
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Handling and analysis of high-throughput microbiome census data title_md: phyloseq - - description_md: '
  • Galaxy tool ids: phyml
  • Description: - PhyML is a phylogeny software based on the maximum-likelihood principle.
  • bio.tool - id: phyml
  • bio.tool ids: phyml
  • biii: - nan
  • bio.tool name: PhyML
  • bio.tool description: - Phylogenetic estimation software using Maximum Likelihood
  • EDAM - operation: Phylogenetic tree generation (maximum likelihood and Bayesian - methods)
  • EDAM topic: Phylogenetics, Bioinformatics, Phylogenetics
  • Status: - Up-to-date
  • Source: http://www.atgc-montpellier.fr/phyml/
  • ToolShed - categories: Phylogenetics
  • ToolShed id: phyml
  • Date - of first commit of the suite: 2019-05-27
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml
  • Galaxy - wrapper version: 3.3.20220408
  • Conda id: phyml
  • Conda - version: 3.3.20220408
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): Phylogenetics, Bioinformatics, - Phylogenetics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1975
  • No. of tool - users (all time) (usegalaxy.eu): 2034
  • Tool usage (5 years) - (usegalaxy.eu): 246
  • Tool usage (all time) (usegalaxy.eu): - 258
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 553
  • No. - of tool users (all time) (usegalaxy.org.au): 564
  • Tool usage - (5 years) (usegalaxy.org.au): 140
  • Tool usage (all time) - (usegalaxy.org.au): 144
  • No. of tool users (5 years) - all - main servers: 2528
  • No. of tool users (all time) - all main - servers: 2598
  • Tool usage (5 years) - all main servers: - 386
  • Tool usage (all time) - all main servers: 402
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: PhyML is a phylogeny software based on the maximum-likelihood + principle. title_md: phyml - - description_md: '
  • 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
  • Description: PICRUSt wrappers
  • bio.tool - id: picrust
  • bio.tool ids: picrust
  • biii: - nan
  • bio.tool name: PICRUSt
  • 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.
  • EDAM - operation: Phylogenetic reconstruction, Expression analysis, Genome annotation, - DNA barcoding
  • EDAM topic: Metagenomics, Microbial ecology, - Functional, regulatory and non-coding RNA, Metagenomic sequencing
  • Status: - To update
  • Source: https://picrust.github.io/picrust/
  • ToolShed - categories: Metagenomics
  • ToolShed id: picrust
  • Date - of first commit of the suite: 2017-07-31
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust
  • Galaxy - wrapper version: 1.1.1
  • Conda id: picrust
  • Conda - version: 1.1.4
  • EDAM operation (no superclasses): - Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding
  • EDAM - topic (no superclasses): Metagenomics, Microbial ecology, Functional, - regulatory and non-coding RNA, Metagenomic sequencing
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 6
  • Available on UseGalaxy.eu: 5
  • Available - on UseGalaxy.fr: 6
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 6
  • Tools - available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: - 6
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 5
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 867
  • No. of tool - users (all time) (usegalaxy.eu): 1128
  • Tool usage (5 years) - (usegalaxy.eu): 144
  • Tool usage (all time) (usegalaxy.eu): - 165
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 2106
  • No. - of tool users (all time) (usegalaxy.org.au): 2106
  • Tool - usage (5 years) (usegalaxy.org.au): 121
  • Tool usage (all - time) (usegalaxy.org.au): 121
  • No. of tool users (5 years) - - all main servers: 2973
  • No. of tool users (all time) - - all main servers: 3234
  • Tool usage (5 years) - all main - servers: 265
  • Tool usage (all time) - all main servers: - 286
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: PICRUSt wrappers title_md: picrust - - description_md: '
  • Galaxy tool ids: picrust2_add_descriptions, - picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, - picrust2_place_seqs, picrust2_shuffle_predictions
  • Description: - PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved - States
  • bio.tool id: picrust2
  • bio.tool ids: - picrust2
  • biii: nan
  • bio.tool name: - PICRUSt2
  • 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.
  • EDAM - operation: Phylogenetic reconstruction, Expression analysis, Rarefaction, - Pathway analysis
  • EDAM topic: Metagenomics, Microbiology, - Phylogenetics, Metagenomic sequencing
  • Status: Up-to-date
  • Source: - https://github.com/picrust/picrust2/wiki
  • ToolShed categories: - Metagenomics
  • ToolShed id: picrust2
  • Date of - first commit of the suite: 2021-11-07
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/picrust/picrust2
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2
  • Galaxy - wrapper version: 2.5.3
  • Conda id: picrust2
  • Conda - version: 2.5.3
  • EDAM operation (no superclasses): - Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis
  • EDAM - topic (no superclasses): Metagenomics, Microbiology, Phylogenetics, Metagenomic - sequencing
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 7
  • Available on UseGalaxy.eu: - 7
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 7
  • Tools available on UseGalaxy.eu: 7
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 2532
  • No. of tool - users (all time) (usegalaxy.eu): 2532
  • Tool usage (5 years) - (usegalaxy.eu): 382
  • Tool usage (all time) (usegalaxy.eu): - 382
  • No. of tool users (5 years) (usegalaxy.org): 1
  • No. - of tool users (all time) (usegalaxy.org): 1
  • Tool usage - (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): - 1
  • No. of tool users (5 years) (usegalaxy.org.au): 1311
  • No. - of tool users (all time) (usegalaxy.org.au): 1311
  • Tool - usage (5 years) (usegalaxy.org.au): 83
  • Tool usage (all - time) (usegalaxy.org.au): 83
  • No. of tool users (5 years) - - all main servers: 3844
  • No. of tool users (all time) - - all main servers: 3844
  • Tool usage (5 years) - all main - servers: 466
  • Tool usage (all time) - all main servers: - 466
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: 'PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction + of Unobserved States' title_md: picrust2 - - description_md: '
  • Galaxy tool ids: PlasFlow
  • Description: - PlasFlow - Prediction of plasmid sequences in metagenomic contigs.
  • bio.tool - id: plasflow
  • bio.tool ids: plasflow
  • biii: - nan
  • bio.tool name: PlasFlow
  • bio.tool description: - PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic - contigs.
  • EDAM operation: Sequence analysis
  • EDAM - topic: Metagenomics
  • Status: Up-to-date
  • Source: - https://github.com/smaegol/PlasFlow
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: plasflow
  • Date - of first commit of the suite: 2018-09-05
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow
  • Galaxy - wrapper version: 1.1.0
  • Conda id: plasflow
  • Conda - version: 1.1.0
  • EDAM operation (no superclasses): - Sequence analysis
  • EDAM topic (no superclasses): Metagenomics
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 37086
  • No. of tool - users (all time) (usegalaxy.eu): 37272
  • Tool usage (5 years) - (usegalaxy.eu): 711
  • Tool usage (all time) (usegalaxy.eu): - 734
  • No. of tool users (5 years) (usegalaxy.org): 6346
  • No. - of tool users (all time) (usegalaxy.org): 6346
  • Tool usage - (5 years) (usegalaxy.org): 583
  • Tool usage (all time) (usegalaxy.org): - 583
  • No. of tool users (5 years) (usegalaxy.org.au): 3065
  • No. - of tool users (all time) (usegalaxy.org.au): 3065
  • Tool - usage (5 years) (usegalaxy.org.au): 61
  • Tool usage (all - time) (usegalaxy.org.au): 61
  • No. of tool users (5 years) - - all main servers: 46497
  • No. of tool users (all time) - - all main servers: 46683
  • Tool usage (5 years) - all main - servers: 1355
  • Tool usage (all time) - all main servers: - 1378
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: PlasFlow - Prediction of plasmid sequences in metagenomic contigs. title_md: plasflow - - description_md: '
  • Galaxy tool ids: plasmidfinder
  • 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"
  • bio.tool - id: PlasmidFinder
  • bio.tool ids: PlasmidFinder
  • biii: - nan
  • bio.tool name: PlasmidFinder
  • bio.tool - description: PlasmidFinder is a tool for the identification and typing - of Plasmid Replicons in Whole-Genome Sequencing (WGS).
  • EDAM operation: - Genome assembly, Scaffolding, Multilocus sequence typing
  • EDAM - topic: Whole genome sequencing, Sequence assembly, Mapping, Probes and - primers
  • Status: Up-to-date
  • Source: - https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: plasmidfinder
  • Date - of first commit of the suite: 2022-09-19
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder
  • Galaxy - wrapper version: 2.1.6
  • Conda id: plasmidfinder
  • Conda - version: 2.1.6
  • EDAM operation (no superclasses): - Genome assembly, Scaffolding, Multilocus sequence typing
  • EDAM - topic (no superclasses): Whole genome sequencing, Sequence assembly, - Mapping, Probes and primers
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 14652
  • No. of tool users (all time) (usegalaxy.eu): 14652
  • Tool - usage (5 years) (usegalaxy.eu): 251
  • Tool usage (all time) - (usegalaxy.eu): 251
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 101
  • No. of tool users (all time) (usegalaxy.org.au): 101
  • Tool - usage (5 years) (usegalaxy.org.au): 18
  • Tool usage (all - time) (usegalaxy.org.au): 18
  • No. of tool users (5 years) - - all main servers: 14753
  • No. of tool users (all time) - - all main servers: 14753
  • Tool usage (5 years) - all main - servers: 269
  • Tool usage (all time) - all main servers: - 269
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: '"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"' title_md: plasmidfinder - - description_md: '
  • Galaxy tool ids: plasmidspades
  • Description: - Genome assembler for assemblying plasmid
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - nan
  • ToolShed categories: Assembly
  • ToolShed - id: plasmidspades
  • Date of first commit of the suite: - 2016-06-06
  • Galaxy wrapper owner: nml
  • Galaxy - wrapper source: nan
  • Galaxy wrapper parsed folder: - https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades
  • Galaxy - wrapper version: 1.1
  • Conda id: spades
  • Conda - version: 4.0.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available 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: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Genome assembler for assemblying plasmid title_md: plasmidspades - - description_md: '
  • Galaxy tool ids: polypolish
  • 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."
  • bio.tool id: - Polypolish
  • bio.tool ids: Polypolish
  • biii: - nan
  • bio.tool name: Polypolish
  • 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.
  • EDAM operation: Genome assembly, Read mapping, - Mapping assembly, Sequencing error detection
  • EDAM topic: - Sequence assembly, Sequence composition, complexity and repeats, Mapping
  • Status: - To update
  • Source: https://github.com/rrwick/Polypolish
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: polypolish
  • Date - of first commit of the suite: 2022-09-22
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish
  • Galaxy - wrapper version: 0.5.0
  • Conda id: polypolish
  • Conda - version: 0.6.0
  • EDAM operation (no superclasses): - Genome assembly, Read mapping, Mapping assembly, Sequencing error detection
  • EDAM - topic (no superclasses): Sequence assembly, Sequence composition, complexity - and repeats, Mapping
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 731
  • No. of tool users (all time) (usegalaxy.eu): 731
  • Tool - usage (5 years) (usegalaxy.eu): 86
  • Tool usage (all time) - (usegalaxy.eu): 86
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 42
  • No. of tool users (all time) (usegalaxy.org.au): 42
  • Tool - usage (5 years) (usegalaxy.org.au): 4
  • Tool usage (all time) - (usegalaxy.org.au): 4
  • No. of tool users (5 years) - all - main servers: 773
  • No. of tool users (all time) - all main - servers: 773
  • Tool usage (5 years) - all main servers: - 90
  • Tool usage (all time) - all main servers: 90
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: '"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."' title_md: polypolish - - description_md: '
  • Galaxy tool ids: prodigal
  • Description: - A protein-coding gene prediction software tool for bacterial and archaeal genomes
  • bio.tool - id: prodigal
  • bio.tool ids: prodigal
  • biii: - nan
  • bio.tool name: Prodigal
  • bio.tool description: - Fast, reliable protein-coding gene prediction for prokaryotic genomes.
  • EDAM - operation: Genome annotation
  • EDAM topic: Genomics, - Sequence analysis
  • Status: Up-to-date
  • Source: - https://github.com/hyattpd/Prodigal
  • ToolShed categories: - Genome annotation
  • ToolShed id: prodigal
  • Date - of first commit of the suite: 2024-03-14
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal
  • Galaxy - wrapper version: 2.6.3
  • Conda id: prodigal
  • Conda - version: 2.6.3
  • EDAM operation (no superclasses): - Genome annotation
  • EDAM topic (no superclasses): Genomics, - Sequence analysis
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1902
  • No. of tool - users (all time) (usegalaxy.eu): 1902
  • Tool usage (5 years) - (usegalaxy.eu): 167
  • Tool usage (all time) (usegalaxy.eu): - 167
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1902
  • No. - of tool users (all time) - all main servers: 1902
  • Tool - usage (5 years) - all main servers: 167
  • Tool usage (all - time) - all main servers: 167
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: A protein-coding gene prediction software tool for bacterial and + archaeal genomes title_md: prodigal - - description_md: '
  • Galaxy tool ids: prokka
  • Description: - Rapid annotation of prokaryotic genomes
  • bio.tool id: prokka
  • bio.tool - ids: prokka
  • biii: nan
  • bio.tool name: - Prokka
  • bio.tool description: Software tool to annotate - bacterial, archaeal and viral genomes quickly and produce standards-compliant - output files.
  • EDAM operation: Gene prediction, Coding region - prediction, Genome annotation
  • EDAM topic: Genomics, Model - organisms, Virology
  • Status: Up-to-date
  • Source: - http://github.com/tseemann/prokka
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: prokka
  • Date - of first commit of the suite: 2016-10-10
  • Galaxy wrapper - owner: crs4
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka
  • Galaxy - wrapper version: 1.14.6
  • Conda id: prokka
  • Conda - version: 1.14.6
  • EDAM operation (no superclasses): - Coding region prediction, Genome annotation
  • EDAM topic (no superclasses): - Genomics, Model organisms, Virology
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 464359
  • No. of tool users (all time) (usegalaxy.eu): 476554
  • Tool - usage (5 years) (usegalaxy.eu): 7475
  • Tool usage (all time) - (usegalaxy.eu): 7721
  • No. of tool users (5 years) (usegalaxy.org): - 313285
  • No. of tool users (all time) (usegalaxy.org): 331256
  • Tool - usage (5 years) (usegalaxy.org): 11243
  • Tool usage (all - time) (usegalaxy.org): 12384
  • No. of tool users (5 years) - (usegalaxy.org.au): 131211
  • No. of tool users (all time) - (usegalaxy.org.au): 141875
  • Tool usage (5 years) (usegalaxy.org.au): - 4358
  • Tool usage (all time) (usegalaxy.org.au): 4947
  • No. - of tool users (5 years) - all main servers: 908855
  • No. - of tool users (all time) - all main servers: 949685
  • Tool - usage (5 years) - all main servers: 23076
  • Tool usage (all - time) - all main servers: 25052
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Rapid annotation of prokaryotic genomes title_md: prokka - - description_md: '
  • Galaxy tool ids: promer4_substitutions
  • Description: - Aligns two sets of contigs and reports amino acid substitutions between them
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: https://github.com/phac-nml/promer
  • ToolShed - categories: Assembly
  • ToolShed id: promer
  • Date - of first commit of the suite: 2019-12-14
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/promer
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer
  • Galaxy - wrapper version: 1.2
  • Conda id: python
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Aligns two sets of contigs and reports amino acid substitutions + between them title_md: promer - - description_md: '
  • Galaxy tool ids: proteinortho, proteinortho_grab_proteins, - proteinortho_summary
  • Description: Proteinortho is a tool - to detect orthologous proteins/genes within different species.
  • bio.tool - id: proteinortho
  • bio.tool ids: proteinortho
  • biii: - nan
  • bio.tool name: Proteinortho
  • bio.tool - description: Proteinortho is a tool to detect orthologous genes within - different species
  • EDAM operation: Sequence clustering, - Sequence analysis
  • EDAM topic: Comparative genomics
  • Status: - To update
  • Source: https://gitlab.com/paulklemm_PHD/proteinortho
  • ToolShed - categories: Proteomics
  • ToolShed id: proteinortho
  • Date - of first commit of the suite: 2020-10-02
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://gitlab.com/paulklemm_PHD/proteinortho
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho
  • Galaxy - wrapper version: 6.3.1
  • Conda id: proteinortho
  • Conda - version: 6.3.2
  • EDAM operation (no superclasses): - Sequence clustering, Sequence analysis
  • EDAM topic (no superclasses): - Comparative genomics
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 3
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 3
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 3962
  • No. of tool users (all time) (usegalaxy.eu): 3962
  • Tool - usage (5 years) (usegalaxy.eu): 501
  • Tool usage (all time) - (usegalaxy.eu): 501
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 3962
  • No. of tool users (all time) - all main - servers: 3962
  • Tool usage (5 years) - all main servers: - 501
  • Tool usage (all time) - all main servers: 501
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Proteinortho is a tool to detect orthologous proteins/genes within + different species. title_md: proteinortho - - description_md: '
  • Galaxy tool ids: pycoqc
  • Description: - QC metrics for ONT Basecalling
  • bio.tool id: pycoqc
  • bio.tool - ids: pycoqc
  • biii: nan
  • bio.tool name: - pycoQC
  • bio.tool description: PycoQC computes metrics and - generates interactive QC plots for Oxford Nanopore technologies sequencing data.
  • EDAM - operation: Sequencing quality control, Statistical calculation
  • EDAM - topic: Sequence analysis, Data quality management, Sequencing
  • Status: - Up-to-date
  • Source: https://github.com/tleonardi/pycoQC
  • ToolShed - categories: Nanopore
  • ToolShed id: pycoqc
  • Date - of first commit of the suite: 2021-03-02
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc
  • Galaxy - wrapper version: 2.5.2
  • Conda id: pycoqc
  • Conda - version: 2.5.2
  • EDAM operation (no superclasses): - Sequencing quality control, Statistical calculation
  • EDAM topic - (no superclasses): Sequence analysis, Data quality management, Sequencing
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 22742
  • No. of tool - users (all time) (usegalaxy.eu): 22742
  • Tool usage (5 years) - (usegalaxy.eu): 557
  • Tool usage (all time) (usegalaxy.eu): - 557
  • No. of tool users (5 years) (usegalaxy.org): 2159
  • No. - of tool users (all time) (usegalaxy.org): 2159
  • Tool usage - (5 years) (usegalaxy.org): 716
  • Tool usage (all time) (usegalaxy.org): - 716
  • No. of tool users (5 years) (usegalaxy.org.au): 776
  • No. - of tool users (all time) (usegalaxy.org.au): 776
  • Tool usage - (5 years) (usegalaxy.org.au): 448
  • Tool usage (all time) - (usegalaxy.org.au): 448
  • No. of tool users (5 years) - all - main servers: 25677
  • No. of tool users (all time) - all - main servers: 25677
  • Tool usage (5 years) - all main servers: - 1721
  • Tool usage (all time) - all main servers: 1721
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: QC metrics for ONT Basecalling title_md: pycoqc - - description_md: '
  • Galaxy tool ids: pygenomeTracks
  • Description: - pyGenomeTracks: Standalone program and library to plot beautiful genome browser - tracks.
  • bio.tool id: pygenometracks
  • bio.tool - ids: pygenometracks
  • biii: nan
  • bio.tool - name: pyGenomeTracks
  • 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:.
  • EDAM operation: Visualisation, Formatting
  • EDAM - topic: Model organisms, Imaging, Workflows
  • Status: - To update
  • Source: https://github.com/deeptools/pyGenomeTracks
  • ToolShed - categories: Visualization
  • ToolShed id: pygenometracks
  • Date - of first commit of the suite: 2020-03-27
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks
  • Galaxy - wrapper version: 3.8
  • Conda id: pygenometracks
  • Conda - version: 3.9
  • EDAM operation (no superclasses): Visualisation, - Formatting
  • EDAM topic (no superclasses): Model organisms, - Imaging, Workflows
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 12858
  • No. of tool - users (all time) (usegalaxy.eu): 13232
  • Tool usage (5 years) - (usegalaxy.eu): 986
  • Tool usage (all time) (usegalaxy.eu): - 996
  • No. of tool users (5 years) (usegalaxy.org): 8092
  • No. - of tool users (all time) (usegalaxy.org): 8092
  • Tool usage - (5 years) (usegalaxy.org): 943
  • Tool usage (all time) (usegalaxy.org): - 943
  • No. of tool users (5 years) (usegalaxy.org.au): 3238
  • No. - of tool users (all time) (usegalaxy.org.au): 3238
  • Tool - usage (5 years) (usegalaxy.org.au): 124
  • Tool usage (all - time) (usegalaxy.org.au): 124
  • No. of tool users (5 years) - - all main servers: 24188
  • No. of tool users (all time) - - all main servers: 24562
  • Tool usage (5 years) - all main - servers: 2053
  • Tool usage (all time) - all main servers: - 2063
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: 'pyGenomeTracks: Standalone program and library to plot beautiful + genome browser tracks.' title_md: pygenometracks - - description_md: '
  • Galaxy tool ids: qiime_collapse_samples, - qiime_make_otu_table
  • Description: QIIME to perform microbial - community analysis
  • bio.tool id: qiime_add_on
  • bio.tool - ids: qiime_core, qiime_add_on
  • biii: nan
  • bio.tool - name: qiime_add_on
  • bio.tool description: QIIME 2 - is a next-generation microbiome bioinformatics platform that is extensible, - free, open source, and community developed.
  • EDAM operation: - Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, - Sequencing quality control
  • EDAM topic: Microbial ecology, - Phylogeny, Metagenomics, Metatranscriptomics
  • Status: To - update
  • Source: http://www.qiime.org
  • ToolShed - categories: Metagenomics
  • ToolShed id: qiime
  • Date - of first commit of the suite: 2017-01-25
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on
  • Galaxy - wrapper version: nan
  • Conda id: qiime
  • Conda - version: 1.9.1
  • EDAM operation (no superclasses): - Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, - Sequencing quality control
  • EDAM topic (no superclasses): - Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 2
  • Available - on UseGalaxy.fr: 2
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 2
  • Tools available on UseGalaxy.fr: - 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 2092
  • No. of tool - users (all time) (usegalaxy.eu): 2342
  • Tool usage (5 years) - (usegalaxy.eu): 209
  • Tool usage (all time) (usegalaxy.eu): - 238
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 2
  • No. - of tool users (all time) (usegalaxy.org.au): 2
  • Tool usage - (5 years) (usegalaxy.org.au): 1
  • Tool usage (all time) (usegalaxy.org.au): - 1
  • No. of tool users (5 years) - all main servers: 2094
  • No. - of tool users (all time) - all main servers: 2344
  • Tool - usage (5 years) - all main servers: 210
  • Tool usage (all - time) - all main servers: 239
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: QIIME to perform microbial community analysis title_md: qiime_add_on - - description_md: "
  • 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
  • Description:\ - \ QIIME to perform microbial community analysis
  • bio.tool id:\ - \ qiime_core
  • bio.tool ids: qiime_core
  • biii:\ - \ nan
  • bio.tool name: qiime_core
  • bio.tool\ - \ description: QIIME 2\u2122 is a next-generation microbiome bioinformatics\ - \ platform that is extensible, free, open source, and community developed.
  • EDAM\ - \ operation: Demultiplexing, Visualisation, Taxonomic classification,\ - \ Phylogenetic analysis, Sequencing quality control
  • EDAM topic:\ - \ Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics
  • Status:\ - \ To update
  • Source: http://www.qiime.org
  • ToolShed\ - \ categories: Metagenomics
  • ToolShed id: qiime
  • Date\ - \ of first commit of the suite: 2017-06-14
  • Galaxy wrapper\ - \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
  • Galaxy\ - \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core
  • Galaxy\ - \ wrapper version: nan
  • Conda id: qiime
  • Conda\ - \ version: 1.9.1
  • EDAM operation (no superclasses):\ - \ Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis,\ - \ Sequencing quality control
  • EDAM topic (no superclasses):\ - \ Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics
  • Available\ - \ on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au:\ - \ 0
  • Available on UseGalaxy.eu: 32
  • Available\ - \ on UseGalaxy.fr: 32
  • Tools available on UseGalaxy.org\ - \ (Main): 0
  • Tools available on UseGalaxy.org.au:\ - \ 0
  • Tools available on UseGalaxy.eu: 32
  • Tools\ - \ available on UseGalaxy.fr: 32
  • Tools available on APOSTL:\ - \ 0
  • Tools available on ARGs-OAP: 0
  • Tools\ - \ available on CIRM-CFBP: 0
  • Tools available on ChemFlow:\ - \ 0
  • Tools available 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.no: 31
  • Tools\ - \ available on Viral Variant Visualizer (VVV): 0
  • No. of\ - \ tool users (5 years) (usegalaxy.eu): 31825
  • No. of tool\ - \ users (all time) (usegalaxy.eu): 34677
  • Tool usage (5\ - \ years) (usegalaxy.eu): 3375
  • Tool usage (all time) (usegalaxy.eu):\ - \ 3785
  • No. of tool users (5 years) (usegalaxy.org): 1
  • No.\ - \ of tool users (all time) (usegalaxy.org): 1
  • Tool usage\ - \ (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org):\ - \ 1
  • No. of tool users (5 years) (usegalaxy.org.au): 14
  • No.\ - \ of tool users (all time) (usegalaxy.org.au): 14
  • Tool\ - \ usage (5 years) (usegalaxy.org.au): 4
  • Tool usage (all\ - \ time) (usegalaxy.org.au): 4
  • No. of tool users (5 years)\ - \ - all main servers: 31840
  • No. of tool users (all time)\ - \ - all main servers: 34692
  • Tool usage (5 years) - all\ - \ main servers: 3380
  • Tool usage (all time) - all main servers:\ - \ 3790
  • Reviewed: True
  • To keep: True
  • Deprecated:\ - \ False
" + - description_md: QIIME to perform microbial community analysis title_md: qiime_core - - description_md: '
  • Galaxy tool ids: qualimap_bamqc, qualimap_counts, - qualimap_multi_bamqc, qualimap_rnaseq
  • 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.
  • bio.tool id: qualimap
  • bio.tool ids: - qualimap
  • biii: nan
  • bio.tool name: - QualiMap
  • 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.
  • EDAM operation: Sequencing quality control
  • EDAM - topic: Data quality management
  • Status: Up-to-date
  • Source: - http://qualimap.bioinfo.cipf.es/
  • ToolShed categories: Sequence - Analysis, Transcriptomics, SAM
  • ToolShed id: qualimap
  • Date - of first commit of the suite: 2019-10-10
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap
  • Galaxy - wrapper version: 2.3
  • Conda id: qualimap
  • Conda - version: 2.3
  • EDAM operation (no superclasses): Sequencing - quality control
  • EDAM topic (no superclasses): Data quality - management
  • Available on UseGalaxy.org (Main): 4
  • Available - on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: - 4
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: - 4
  • Tools available on UseGalaxy.eu: 4
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 4
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 684820
  • No. of tool - users (all time) (usegalaxy.eu): 684820
  • Tool usage (5 years) - (usegalaxy.eu): 3239
  • Tool usage (all time) (usegalaxy.eu): - 3239
  • No. of tool users (5 years) (usegalaxy.org): 90503
  • No. - of tool users (all time) (usegalaxy.org): 90503
  • Tool usage - (5 years) (usegalaxy.org): 3881
  • Tool usage (all time) (usegalaxy.org): - 3881
  • No. of tool users (5 years) (usegalaxy.org.au): 29018
  • No. - of tool users (all time) (usegalaxy.org.au): 29018
  • Tool - usage (5 years) (usegalaxy.org.au): 826
  • Tool usage (all - time) (usegalaxy.org.au): 826
  • No. of tool users (5 years) - - all main servers: 804341
  • No. of tool users (all time) - - all main servers: 804341
  • Tool usage (5 years) - all main - servers: 7946
  • Tool usage (all time) - all main servers: - 7946
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: 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. title_md: qualimap - - description_md: '
  • Galaxy tool ids: quast
  • Description: - Quast (Quality ASsessment Tool) evaluates genome assemblies.
  • bio.tool - id: quast
  • bio.tool ids: quast
  • biii: - nan
  • bio.tool name: QUAST
  • bio.tool description: - QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome - assemblies by computing various metrics and providing nice reports.
  • EDAM - operation: Visualisation, Sequence assembly validation
  • EDAM - topic: Sequence assembly
  • Status: Up-to-date
  • Source: - http://quast.bioinf.spbau.ru/
  • ToolShed categories: Assembly
  • ToolShed - id: quast
  • Date of first commit of the suite: 2018-02-10
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast
  • Galaxy - wrapper version: 5.2.0
  • Conda id: quast
  • Conda - version: 5.2.0
  • EDAM operation (no superclasses): - Visualisation, Sequence assembly validation
  • EDAM topic (no superclasses): - Sequence assembly
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 67737
  • No. of tool - users (all time) (usegalaxy.eu): 69738
  • Tool usage (5 years) - (usegalaxy.eu): 7787
  • Tool usage (all time) (usegalaxy.eu): - 7971
  • No. of tool users (5 years) (usegalaxy.org): 51925
  • No. - of tool users (all time) (usegalaxy.org): 56602
  • Tool usage - (5 years) (usegalaxy.org): 9692
  • Tool usage (all time) (usegalaxy.org): - 10646
  • No. of tool users (5 years) (usegalaxy.org.au): 32003
  • No. - of tool users (all time) (usegalaxy.org.au): 34145
  • Tool - usage (5 years) (usegalaxy.org.au): 3890
  • Tool usage (all - time) (usegalaxy.org.au): 4127
  • No. of tool users (5 years) - - all main servers: 151665
  • No. of tool users (all time) - - all main servers: 160485
  • Tool usage (5 years) - all main - servers: 21369
  • Tool usage (all time) - all main servers: - 22744
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Quast (Quality ASsessment Tool) evaluates genome assemblies. title_md: quast - - description_md: '
  • Galaxy tool ids: quickmerge
  • Description: - Merge long-read and hybrid assemblies to increase contiguity
  • bio.tool - id: quickmerge
  • bio.tool ids: quickmerge
  • biii: - nan
  • bio.tool name: quickmerge
  • 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.
  • EDAM - operation: Genome assembly, Scaffolding, De-novo assembly, Genotyping
  • EDAM - topic: Structural variation, Sequence assembly, DNA polymorphism, Whole - genome sequencing, Genotype and phenotype
  • Status: Up-to-date
  • Source: - https://github.com/mahulchak/quickmerge
  • ToolShed categories: - Assembly
  • ToolShed id: quickmerge
  • Date of - first commit of the suite: 2022-07-08
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge
  • Galaxy - wrapper version: 0.3
  • Conda id: quickmerge
  • Conda - version: 0.3
  • EDAM operation (no superclasses): Genome - assembly, Scaffolding, De-novo assembly, Genotyping
  • EDAM topic - (no superclasses): Structural variation, Sequence assembly, DNA polymorphism, - Whole genome sequencing, Genotype and phenotype
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Merge long-read and hybrid assemblies to increase contiguity title_md: quickmerge - - description_md: '
  • Galaxy tool ids: meta_rna
  • Description: - Identification of ribosomal RNA genes in metagenomic fragments.
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: http://weizhong-lab.ucsd.edu/meta_rna/
  • ToolShed - categories: RNA
  • ToolShed id: rrna
  • Date - of first commit of the suite: 2015-02-28
  • Galaxy wrapper - owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rRNA
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA
  • Galaxy - wrapper version: 0.1
  • Conda id: hmmsearch3.0
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Identification of ribosomal RNA genes in metagenomic fragments. title_md: rRNA - - description_md: '
  • Galaxy tool ids: racon
  • Description: - Consensus module for raw de novo DNA assembly of long uncorrected reads.
  • bio.tool - id: Racon
  • bio.tool ids: Racon
  • biii: - nan
  • bio.tool name: Racon
  • 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.
  • EDAM operation: Genome assembly, - Mapping assembly
  • EDAM topic: Whole genome sequencing, Sequence - assembly
  • Status: Up-to-date
  • Source: - https://github.com/isovic/racon
  • ToolShed categories: Sequence - Analysis
  • ToolShed id: racon
  • Date of first - commit of the suite: 2018-06-11
  • Galaxy wrapper owner: - bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/racon
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/racon
  • Galaxy - wrapper version: 1.5.0
  • Conda id: racon
  • Conda - version: 1.5.0
  • EDAM operation (no superclasses): - Genome assembly, Mapping assembly
  • EDAM topic (no superclasses): - Whole genome sequencing, Sequence assembly
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 27113
  • No. of tool users (all time) (usegalaxy.eu): 27315
  • Tool - usage (5 years) (usegalaxy.eu): 839
  • Tool usage (all time) - (usegalaxy.eu): 850
  • No. of tool users (5 years) (usegalaxy.org): - 9089
  • No. of tool users (all time) (usegalaxy.org): 9089
  • Tool - usage (5 years) (usegalaxy.org): 475
  • Tool usage (all time) - (usegalaxy.org): 475
  • No. of tool users (5 years) (usegalaxy.org.au): - 5452
  • No. of tool users (all time) (usegalaxy.org.au): 5452
  • Tool - usage (5 years) (usegalaxy.org.au): 171
  • Tool usage (all - time) (usegalaxy.org.au): 171
  • No. of tool users (5 years) - - all main servers: 41654
  • No. of tool users (all time) - - all main servers: 41856
  • Tool usage (5 years) - all main - servers: 1485
  • Tool usage (all time) - all main servers: - 1496
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Consensus module for raw de novo DNA assembly of long uncorrected + reads. title_md: racon - - description_md: '
  • Galaxy tool ids: rasusa
  • Description: - Randomly subsample sequencing reads to a specified coverage
  • bio.tool - id: rasusa
  • bio.tool ids: rasusa
  • biii: - nan
  • bio.tool name: rasusa
  • bio.tool description: - Produces an unbiased subsample of your reads
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://github.com/mbhall88/rasusa
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: rasusa
  • Date - of first commit of the suite: 2024-02-16
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa
  • Galaxy - wrapper version: 2.0.0
  • Conda id: rasusa
  • Conda - version: 2.1.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 42
  • No. of tool - users (all time) (usegalaxy.eu): 42
  • Tool usage (5 years) - (usegalaxy.eu): 9
  • Tool usage (all time) (usegalaxy.eu): - 9
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 42
  • No. - of tool users (all time) - all main servers: 42
  • Tool usage - (5 years) - all main servers: 9
  • Tool usage (all time) - - all main servers: 9
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Randomly subsample sequencing reads to a specified coverage title_md: rasusa - - description_md: '
  • Galaxy tool ids: raxml
  • Description: - RAxML - A Maximum Likelihood based phylogenetic inference
  • bio.tool - id: raxml
  • bio.tool ids: raxml
  • biii: - nan
  • bio.tool name: RAxML
  • bio.tool description: - A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
  • EDAM - operation: Sequence analysis, Phylogenetic tree analysis
  • EDAM - topic: Phylogenetics, Sequence analysis
  • Status: - To update
  • Source: http://www.exelixis-lab.org/web/software/raxml/
  • ToolShed - categories: Phylogenetics
  • ToolShed id: raxml
  • Date - of first commit of the suite: 2015-11-05
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml
  • Galaxy - wrapper version: 8.2.12
  • Conda id: raxml
  • Conda - version: 8.2.13
  • EDAM operation (no superclasses): - Sequence analysis
  • EDAM topic (no superclasses): Phylogenetics
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 10905
  • No. of tool - users (all time) (usegalaxy.eu): 10905
  • Tool usage (5 years) - (usegalaxy.eu): 966
  • Tool usage (all time) (usegalaxy.eu): - 966
  • No. of tool users (5 years) (usegalaxy.org): 5100
  • No. - of tool users (all time) (usegalaxy.org): 5114
  • Tool usage - (5 years) (usegalaxy.org): 587
  • Tool usage (all time) (usegalaxy.org): - 587
  • No. of tool users (5 years) (usegalaxy.org.au): 4955
  • No. - of tool users (all time) (usegalaxy.org.au): 6094
  • Tool - usage (5 years) (usegalaxy.org.au): 765
  • Tool usage (all - time) (usegalaxy.org.au): 892
  • No. of tool users (5 years) - - all main servers: 20960
  • No. of tool users (all time) - - all main servers: 22113
  • Tool usage (5 years) - all main - servers: 2318
  • Tool usage (all time) - all main servers: - 2445
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: RAxML - A Maximum Likelihood based phylogenetic inference title_md: raxml - - description_md: '
  • Galaxy tool ids: read_it_and_keep
  • Description: - Rapid decontamination of SARS-CoV-2 sequencing reads
  • bio.tool - id: read_it_and_keep
  • bio.tool ids: read_it_and_keep
  • biii: - nan
  • bio.tool name: read_it_and_keep
  • bio.tool - description: Read contamination removal
  • EDAM operation: - Filtering, Genome alignment
  • EDAM topic: Pathology, Genomics
  • Status: - To update
  • Source: https://github.com/GenomePathogenAnalysisService/read-it-and-keep
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: read_it_and_keep
  • Date - of first commit of the suite: 2022-01-28
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep
  • Galaxy - wrapper version: 0.2.2
  • Conda id: read-it-and-keep
  • Conda - version: 0.3.0
  • EDAM operation (no superclasses): - Filtering, Genome alignment
  • EDAM topic (no superclasses): - Pathology, Genomics
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 3710
  • No. of tool users (all time) (usegalaxy.eu): 3710
  • Tool - usage (5 years) (usegalaxy.eu): 80
  • Tool usage (all time) - (usegalaxy.eu): 80
  • No. of tool users (5 years) (usegalaxy.org): - 7
  • No. of tool users (all time) (usegalaxy.org): 7
  • Tool - usage (5 years) (usegalaxy.org): 6
  • Tool usage (all time) - (usegalaxy.org): 6
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 3717
  • No. of tool users (all time) - all main - servers: 3717
  • Tool usage (5 years) - all main servers: - 86
  • Tool usage (all time) - all main servers: 86
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Rapid decontamination of SARS-CoV-2 sequencing reads title_md: read_it_and_keep - - description_md: '
  • Galaxy tool ids: reago
  • Description: - Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.
  • bio.tool - id: reago
  • bio.tool ids: reago
  • biii: - nan
  • bio.tool name: REAGO
  • bio.tool description: - This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.
  • EDAM - operation: Sequence assembly
  • EDAM topic: Sequence - assembly, RNA, Metagenomics, Microbiology
  • Status: Up-to-date
  • Source: - https://github.com/chengyuan/reago-1.1
  • ToolShed categories: - Metagenomics, RNA
  • ToolShed id: reago
  • Date - of first commit of the suite: 2015-12-09
  • Galaxy wrapper - owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago
  • Galaxy - wrapper version: 1.1
  • Conda id: reago
  • Conda - version: 1.1
  • EDAM operation (no superclasses): Sequence - assembly
  • EDAM topic (no superclasses): Sequence assembly, - RNA, Metagenomics, Microbiology
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic + data. title_md: reago - - description_md: '
  • Galaxy tool ids: recentrifuge
  • 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."
  • bio.tool - id: Recentrifuge
  • bio.tool ids: Recentrifuge
  • biii: - nan
  • bio.tool name: Recentrifuge
  • bio.tool - description: Robust comparative analysis and contamination removal for - metagenomics.
  • EDAM operation: Taxonomic classification, - Expression analysis, Cross-assembly
  • EDAM topic: Metagenomics, - Microbial ecology, Metagenomic sequencing
  • Status: Up-to-date
  • Source: - https://github.com/khyox/recentrifuge
  • ToolShed categories: - Metagenomics
  • ToolShed id: recentrifuge
  • Date - of first commit of the suite: 2022-05-04
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge
  • Galaxy - wrapper version: 1.15.0
  • Conda id: recentrifuge
  • Conda - version: 1.15.0
  • EDAM operation (no superclasses): - Taxonomic classification, Expression analysis, Cross-assembly
  • EDAM - topic (no superclasses): Metagenomics, Microbial ecology, Metagenomic - sequencing
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 472
  • No. of tool - users (all time) (usegalaxy.eu): 472
  • Tool usage (5 years) - (usegalaxy.eu): 92
  • Tool usage (all time) (usegalaxy.eu): - 92
  • No. of tool users (5 years) (usegalaxy.org): 32
  • No. - of tool users (all time) (usegalaxy.org): 32
  • Tool usage - (5 years) (usegalaxy.org): 13
  • Tool usage (all time) (usegalaxy.org): - 13
  • No. of tool users (5 years) (usegalaxy.org.au): 6
  • No. - of tool users (all time) (usegalaxy.org.au): 6
  • Tool usage - (5 years) (usegalaxy.org.au): 4
  • Tool usage (all time) (usegalaxy.org.au): - 4
  • No. of tool users (5 years) - all main servers: 510
  • No. - of tool users (all time) - all main servers: 510
  • Tool usage - (5 years) - all main servers: 109
  • Tool usage (all time) - - all main servers: 109
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: '"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."' title_md: recentrifuge - - description_md: '
  • Galaxy tool ids: repeatexplorer_clustering
  • Description: - Tool for annotation of repeats from unassembled shotgun reads.
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: https://github.com/repeatexplorer/repex_tarean
  • ToolShed - categories: Genome annotation
  • ToolShed id: repeatexplorer2
  • Date - of first commit of the suite: 2023-11-01
  • Galaxy wrapper - owner: gga
  • Galaxy wrapper source: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2
  • Galaxy - wrapper parsed folder: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2
  • Galaxy - wrapper version: 2.3.8
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 95
  • No. of tool users (all time) (usegalaxy.eu): 95
  • Tool - usage (5 years) (usegalaxy.eu): 38
  • Tool usage (all time) - (usegalaxy.eu): 38
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 95
  • No. of tool users (all time) - all main - servers: 95
  • Tool usage (5 years) - all main servers: - 38
  • Tool usage (all time) - all main servers: 38
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Tool for annotation of repeats from unassembled shotgun reads. title_md: repeatexplorer2 - - description_md: '
  • Galaxy tool ids: roary
  • Description: - Roary the pangenome pipeline
  • bio.tool id: roary
  • bio.tool - ids: roary
  • biii: nan
  • bio.tool name: - Roary
  • 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.
  • EDAM operation: - Genome assembly
  • EDAM topic: DNA, Genomics, Mapping
  • Status: - Up-to-date
  • Source: https://sanger-pathogens.github.io/Roary/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: roary
  • Date - of first commit of the suite: 2017-06-21
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary
  • Galaxy - wrapper version: 3.13.0
  • Conda id: roary
  • Conda - version: 3.13.0
  • EDAM operation (no superclasses): - Genome assembly
  • EDAM topic (no superclasses): DNA, Genomics, - Mapping
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 15196
  • No. of tool - users (all time) (usegalaxy.eu): 15685
  • Tool usage (5 years) - (usegalaxy.eu): 1459
  • Tool usage (all time) (usegalaxy.eu): - 1501
  • No. of tool users (5 years) (usegalaxy.org): 12188
  • No. - of tool users (all time) (usegalaxy.org): 12188
  • Tool usage - (5 years) (usegalaxy.org): 1768
  • Tool usage (all time) (usegalaxy.org): - 1768
  • No. of tool users (5 years) (usegalaxy.org.au): 4881
  • No. - of tool users (all time) (usegalaxy.org.au): 5539
  • Tool - usage (5 years) (usegalaxy.org.au): 518
  • Tool usage (all - time) (usegalaxy.org.au): 555
  • No. of tool users (5 years) - - all main servers: 32265
  • No. of tool users (all time) - - all main servers: 33412
  • Tool usage (5 years) - all main - servers: 3745
  • Tool usage (all time) - all main servers: - 3824
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Roary the pangenome pipeline title_md: roary - - description_md: '
  • 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
  • Description: - an RNA-seq quality control package
  • bio.tool id: rseqc
  • bio.tool - ids: rseqc
  • biii: nan
  • bio.tool name: - RSeQC
  • 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.
  • EDAM operation: - Data handling
  • EDAM topic: Sequencing
  • Status: - To update
  • Source: https://code.google.com/p/rseqc/
  • ToolShed - categories: Convert Formats, Sequence Analysis, RNA, Transcriptomics, - Visualization
  • ToolShed id: rseqc
  • Date of - first commit of the suite: 2017-02-27
  • Galaxy wrapper owner: - nilesh
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc
  • Galaxy - wrapper version: 5.0.3
  • Conda id: rseqc
  • Conda - version: 5.0.4
  • EDAM operation (no superclasses): - Data handling
  • EDAM topic (no superclasses): Sequencing
  • Available - on UseGalaxy.org (Main): 22
  • Available on UseGalaxy.org.au: - 22
  • Available on UseGalaxy.eu: 22
  • Available - on UseGalaxy.fr: 22
  • Tools available on UseGalaxy.org (Main): - 22
  • Tools available on UseGalaxy.org.au: 22
  • Tools - available on UseGalaxy.eu: 22
  • Tools available on UseGalaxy.fr: - 22
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 22
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 136315
  • No. of tool - users (all time) (usegalaxy.eu): 147595
  • Tool usage (5 years) - (usegalaxy.eu): 8341
  • Tool usage (all time) (usegalaxy.eu): - 9385
  • No. of tool users (5 years) (usegalaxy.org): 138707
  • No. - of tool users (all time) (usegalaxy.org): 161046
  • Tool usage - (5 years) (usegalaxy.org): 10696
  • Tool usage (all time) - (usegalaxy.org): 12789
  • No. of tool users (5 years) (usegalaxy.org.au): - 22718
  • No. of tool users (all time) (usegalaxy.org.au): - 23767
  • Tool usage (5 years) (usegalaxy.org.au): 1593
  • Tool - usage (all time) (usegalaxy.org.au): 1695
  • No. of tool users - (5 years) - all main servers: 297740
  • No. of tool users - (all time) - all main servers: 332408
  • Tool usage (5 years) - - all main servers: 20630
  • Tool usage (all time) - all main - servers: 23869
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: an RNA-seq quality control package title_md: rseqc - - description_md: '
  • Galaxy tool ids: alevin, salmon, salmonquantmerge
  • Description: - Salmon is a wicked-fast program to produce a highly-accurate, transcript-level - quantification estimates from RNA-seq and single-cell data.
  • bio.tool - id: salmon
  • bio.tool ids: salmon
  • biii: - nan
  • bio.tool name: Salmon
  • bio.tool description: - A tool for transcript expression quantification from RNA-seq data
  • EDAM - operation: Sequence composition calculation, RNA-Seq quantification, - Gene expression analysis
  • EDAM topic: RNA-Seq, Gene expression, - Transcriptomics
  • Status: To update
  • Source: - https://github.com/COMBINE-lab/salmon
  • ToolShed categories: - Sequence Analysis, RNA, Transcriptomics
  • ToolShed id: nan
  • Date - of first commit of the suite: 2019-09-18
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/salmon
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/salmon
  • Galaxy - wrapper version: 1.10.1
  • Conda id: salmon
  • Conda - version: 1.10.3
  • EDAM operation (no superclasses): - Sequence composition calculation, RNA-Seq quantification, Gene expression analysis
  • EDAM - topic (no superclasses): RNA-Seq, Transcriptomics
  • Available - on UseGalaxy.org (Main): 2
  • Available on UseGalaxy.org.au: - 2
  • Available on UseGalaxy.eu: 3
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 2
  • Tools available on UseGalaxy.org.au: 2
  • Tools - available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available 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.no: - 3
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 73085
  • No. of tool - users (all time) (usegalaxy.eu): 77081
  • Tool usage (5 years) - (usegalaxy.eu): 2243
  • Tool usage (all time) (usegalaxy.eu): - 2319
  • No. of tool users (5 years) (usegalaxy.org): 90634
  • No. - of tool users (all time) (usegalaxy.org): 122835
  • Tool usage - (5 years) (usegalaxy.org): 3402
  • Tool usage (all time) (usegalaxy.org): - 4726
  • No. of tool users (5 years) (usegalaxy.org.au): 13371
  • No. - of tool users (all time) (usegalaxy.org.au): 15818
  • Tool - usage (5 years) (usegalaxy.org.au): 513
  • Tool usage (all - time) (usegalaxy.org.au): 586
  • No. of tool users (5 years) - - all main servers: 177090
  • No. of tool users (all time) - - all main servers: 215734
  • Tool usage (5 years) - all main - servers: 6158
  • Tool usage (all time) - all main servers: - 7631
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq and single-cell data. title_md: salmon - - description_md: '
  • Galaxy tool ids: sarscov2formatter
  • Description: - sarscov2formatter custom script
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: - https://github.com/nickeener/sarscov2formatter
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: sarscov2formatter
  • Date - of first commit of the suite: 2020-05-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter
  • Galaxy - wrapper version: 1.0
  • Conda id: sarscov2formatter
  • Conda - version: 1.0
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 174
  • No. of tool users (all time) (usegalaxy.eu): 174
  • Tool - usage (5 years) (usegalaxy.eu): 16
  • Tool usage (all time) - (usegalaxy.eu): 16
  • No. of tool users (5 years) (usegalaxy.org): - 399
  • No. of tool users (all time) (usegalaxy.org): 399
  • Tool - usage (5 years) (usegalaxy.org): 29
  • Tool usage (all time) - (usegalaxy.org): 29
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 573
  • No. of tool users (all time) - all main - servers: 573
  • Tool usage (5 years) - all main servers: - 45
  • Tool usage (all time) - all main servers: 45
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: sarscov2formatter custom script title_md: sarscov2formatter - - description_md: '
  • Galaxy tool ids: sarscov2summary
  • Description: - sarscov2summary custom script
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://github.com/nickeener/sarscov2summary
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: sarscov2summary
  • Date - of first commit of the suite: 2020-05-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary
  • Galaxy - wrapper version: 0.1
  • Conda id: sarscov2summary
  • Conda - version: 0.5
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 140
  • No. of tool users (all time) (usegalaxy.eu): 140
  • Tool - usage (5 years) (usegalaxy.eu): 5
  • Tool usage (all time) - (usegalaxy.eu): 5
  • No. of tool users (5 years) (usegalaxy.org): - 253
  • No. of tool users (all time) (usegalaxy.org): 253
  • Tool - usage (5 years) (usegalaxy.org): 6
  • Tool usage (all time) - (usegalaxy.org): 6
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 393
  • No. of tool users (all time) - all main - servers: 393
  • Tool usage (5 years) - all main servers: - 11
  • Tool usage (all time) - all main servers: 11
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: sarscov2summary custom script title_md: sarscov2summary - - description_md: '
  • Galaxy tool ids: scoary
  • Description: - Scoary calculates the assocations between all genes in the accessory genome - and the traits.
  • bio.tool id: scoary
  • bio.tool - ids: scoary
  • biii: nan
  • bio.tool name: - Scoary
  • 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.
  • EDAM operation: Analysis
  • EDAM - topic: Genotype and phenotype, Model organisms, GWAS study, Functional - genomics
  • Status: Up-to-date
  • Source: - https://github.com/AdmiralenOla/Scoary
  • ToolShed categories: - Metagenomics
  • ToolShed id: scoary
  • Date of - first commit of the suite: 2021-03-18
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary
  • Galaxy - wrapper version: 1.6.16
  • Conda id: scoary
  • Conda - version: 1.6.16
  • EDAM operation (no superclasses): - Analysis
  • EDAM topic (no superclasses): Genotype and phenotype, - Model organisms, GWAS study, Functional genomics
  • Available on - UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 901
  • No. of tool - users (all time) (usegalaxy.eu): 901
  • Tool usage (5 years) - (usegalaxy.eu): 90
  • Tool usage (all time) (usegalaxy.eu): - 90
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 901
  • No. - of tool users (all time) - all main servers: 901
  • Tool usage - (5 years) - all main servers: 90
  • Tool usage (all time) - - all main servers: 90
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Scoary calculates the assocations between all genes in the accessory + genome and the traits. title_md: scoary - - description_md: '
  • Galaxy tool ids: semibin_bin, semibin_concatenate_fasta, - semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, - semibin_train
  • Description: SemiBin: Semi-supervised Metagenomic - Binning Using Siamese Neural Networks
  • bio.tool id: semibin
  • bio.tool - ids: semibin
  • biii: nan
  • bio.tool name: - SemiBin
  • bio.tool description: Command tool for metagenomic - binning with semi-supervised deep learning using information from reference - genomes.
  • EDAM operation: Sequence assembly, Read binning
  • EDAM - topic: Metagenomics, Machine learning, Microbial ecology, Sequence assembly
  • Status: - To update
  • Source: https://semibin.readthedocs.io/en/latest/
  • ToolShed - categories: Metagenomics
  • ToolShed id: semibin
  • Date - of first commit of the suite: 2022-10-14
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin
  • Galaxy - wrapper version: 2.0.2
  • Conda id: semibin
  • Conda - version: 2.1.0
  • EDAM operation (no superclasses): - Sequence assembly, Read binning
  • EDAM topic (no superclasses): - Metagenomics, Machine learning, Microbial ecology, Sequence assembly
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 6
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 6
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 931
  • No. of tool - users (all time) (usegalaxy.eu): 931
  • Tool usage (5 years) - (usegalaxy.eu): 93
  • Tool usage (all time) (usegalaxy.eu): - 93
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 931
  • No. - of tool users (all time) - all main servers: 931
  • Tool usage - (5 years) - all main servers: 93
  • Tool usage (all time) - - all main servers: 93
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: 'SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural + Networks' title_md: semibin - - description_md: '
  • Galaxy tool ids: seqkit_fx2tab, seqkit_locate, - seqkit_sort, seqkit_stats, seqkit_translate
  • Description: - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  • bio.tool - id: seqkit
  • bio.tool ids: seqkit
  • biii: - nan
  • bio.tool name: seqkit
  • 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.
  • EDAM operation: DNA - transcription, Sequence trimming, DNA translation, Sequence conversion
  • EDAM - topic: Database management, Sequence analysis
  • Status: - Up-to-date
  • Source: https://bioinf.shenwei.me/seqkit/
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: seqkit
  • Date - of first commit of the suite: 2022-06-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit
  • Galaxy - wrapper version: 2.8.2
  • Conda id: seqkit
  • Conda - version: 2.8.2
  • EDAM operation (no superclasses): - DNA transcription, Sequence trimming, DNA translation
  • EDAM topic - (no superclasses): Database management, Sequence analysis
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 2
  • Available on UseGalaxy.eu: 5
  • Available - on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 2
  • Tools - available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: - 3
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 3364
  • No. of tool - users (all time) (usegalaxy.eu): 3364
  • Tool usage (5 years) - (usegalaxy.eu): 247
  • Tool usage (all time) (usegalaxy.eu): - 247
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 244
  • No. - of tool users (all time) (usegalaxy.org.au): 244
  • Tool usage - (5 years) (usegalaxy.org.au): 33
  • Tool usage (all time) - (usegalaxy.org.au): 33
  • No. of tool users (5 years) - all - main servers: 3608
  • No. of tool users (all time) - all main - servers: 3608
  • Tool usage (5 years) - all main servers: - 280
  • Tool usage (all time) - all main servers: 280
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation title_md: seqkit - - description_md: '
  • Galaxy tool ids: seqprep
  • Description: - Tool for merging paired-end Illumina reads and trimming adapters.
  • bio.tool - id: seqprep
  • bio.tool ids: seqprep
  • biii: - nan
  • bio.tool name: SeqPrep
  • bio.tool description: - Strips adapters and optionally merges overlapping paired-end (or paired-end - contamination in mate-pair libraries) illumina style reads.
  • EDAM - operation: Nucleic acid design
  • EDAM topic: Genomics, - Sequence assembly, Sequencing, Probes and primers
  • Status: - Up-to-date
  • Source: https://github.com/jstjohn/SeqPrep
  • ToolShed - categories: Fastq Manipulation, Sequence Analysis
  • ToolShed - id: seqprep
  • Date of first commit of the suite: 2024-01-15
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep
  • Galaxy - wrapper version: 1.3.2
  • Conda id: seqprep
  • Conda - version: 1.3.2
  • EDAM operation (no superclasses): - Nucleic acid design
  • EDAM topic (no superclasses): Genomics, - Sequence assembly, Sequencing, Probes and primers
  • Available on - UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 2424
  • No. of tool - users (all time) (usegalaxy.eu): 2424
  • Tool usage (5 years) - (usegalaxy.eu): 102
  • Tool usage (all time) (usegalaxy.eu): - 102
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 2424
  • No. - of tool users (all time) - all main servers: 2424
  • Tool - usage (5 years) - all main servers: 102
  • Tool usage (all - time) - all main servers: 102
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Tool for merging paired-end Illumina reads and trimming adapters. title_md: seqprep - - description_md: '
  • Galaxy tool ids: seqsero2
  • Description: - Salmonella serotype prediction from genome sequencing data
  • bio.tool - id: seqsero2
  • bio.tool ids: seqsero2
  • biii: - nan
  • bio.tool name: SeqSero2
  • 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)
  • EDAM operation: Genome indexing, Antimicrobial - resistance prediction, Genome alignment
  • EDAM topic: Whole - genome sequencing, Sequence assembly, Genomics
  • Status: - Up-to-date
  • Source: https://github.com/denglab/SeqSero2
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: seqsero2
  • Date - of first commit of the suite: 2023-11-07
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2
  • Galaxy - wrapper version: 1.3.1
  • Conda id: seqsero2
  • Conda - version: 1.3.1
  • EDAM operation (no superclasses): - Genome indexing, Antimicrobial resistance prediction, Genome alignment
  • EDAM - topic (no superclasses): Whole genome sequencing, Sequence assembly, - Genomics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 4182
  • No. of tool - users (all time) (usegalaxy.eu): 4182
  • Tool usage (5 years) - (usegalaxy.eu): 42
  • Tool usage (all time) (usegalaxy.eu): - 42
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 4182
  • No. - of tool users (all time) - all main servers: 4182
  • Tool - usage (5 years) - all main servers: 42
  • Tool usage (all - time) - all main servers: 42
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Salmonella serotype prediction from genome sequencing data title_md: seqsero2 - - description_md: '
  • Galaxy tool ids: shorah_amplicon
  • Description: - Reconstruct haplotypes using ShoRAH in amplicon mode
  • bio.tool - id: shorah
  • bio.tool ids: shorah
  • biii: - nan
  • bio.tool name: ShoRAH
  • 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.
  • EDAM operation: - Haplotype mapping, Variant calling
  • EDAM topic: Metagenomics, - Sequencing, Genetics
  • Status: To update
  • Source: - https://github.com/cbg-ethz/shorah/blob/master/README.md
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: shorah_amplicon
  • Date - of first commit of the suite: 2018-11-27
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah
  • Galaxy - wrapper version: 1.1.3
  • Conda id: shorah
  • Conda - version: 1.99.2
  • EDAM operation (no superclasses): - Haplotype mapping, Variant calling
  • EDAM topic (no superclasses): - Metagenomics, Sequencing, Genetics
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
  • Tool usage (all time) - (usegalaxy.eu): 0
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Reconstruct haplotypes using ShoRAH in amplicon mode title_md: shorah - - description_md: '
  • Galaxy tool ids: shovill
  • Description: - Faster de novo assembly pipeline based around Spades
  • bio.tool - id: shovill
  • bio.tool ids: shovill
  • biii: - nan
  • bio.tool name: shovill
  • 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.
  • EDAM - operation: Genome assembly
  • EDAM topic: Genomics, - Microbiology, Sequence assembly
  • Status: Up-to-date
  • Source: - https://github.com/tseemann/shovill
  • ToolShed categories: - Assembly
  • ToolShed id: shovill
  • Date of first - commit of the suite: 2017-10-24
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill
  • Galaxy - wrapper version: 1.1.0
  • Conda id: shovill
  • Conda - version: 1.1.0
  • EDAM operation (no superclasses): - Genome assembly
  • EDAM topic (no superclasses): Genomics, - Microbiology, Sequence assembly
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 46125
  • No. of tool users (all time) (usegalaxy.eu): 47376
  • Tool - usage (5 years) (usegalaxy.eu): 2273
  • Tool usage (all time) - (usegalaxy.eu): 2356
  • No. of tool users (5 years) (usegalaxy.org): - 40577
  • No. of tool users (all time) (usegalaxy.org): 40577
  • Tool - usage (5 years) (usegalaxy.org): 3971
  • Tool usage (all time) - (usegalaxy.org): 3971
  • No. of tool users (5 years) (usegalaxy.org.au): - 19960
  • No. of tool users (all time) (usegalaxy.org.au): - 21130
  • Tool usage (5 years) (usegalaxy.org.au): 1085
  • Tool - usage (all time) (usegalaxy.org.au): 1199
  • No. of tool users - (5 years) - all main servers: 106662
  • No. of tool users - (all time) - all main servers: 109083
  • Tool usage (5 years) - - all main servers: 7329
  • Tool usage (all time) - all main - servers: 7526
  • Reviewed: True
  • To keep: - True
  • Deprecated: False
' + - description_md: Faster de novo assembly pipeline based around Spades title_md: shovill - - description_md: '
  • Galaxy tool ids: sistr_cmd
  • Description: - SISTR in silico serotyping tool
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://github.com/phac-nml/sistr_cmd
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: sistr_cmd
  • Date - of first commit of the suite: 2017-02-20
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: nan
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd
  • Galaxy - wrapper version: 1.1.1
  • Conda id: sistr_cmd
  • Conda - version: 1.1.2
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 3457
  • No. of tool - users (all time) (usegalaxy.eu): 3457
  • Tool usage (5 years) - (usegalaxy.eu): 301
  • Tool usage (all time) (usegalaxy.eu): - 301
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 556
  • No. - of tool users (all time) (usegalaxy.org.au): 556
  • Tool usage - (5 years) (usegalaxy.org.au): 65
  • Tool usage (all time) - (usegalaxy.org.au): 65
  • No. of tool users (5 years) - all - main servers: 4013
  • No. of tool users (all time) - all main - servers: 4013
  • Tool usage (5 years) - all main servers: - 366
  • Tool usage (all time) - all main servers: 366
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: SISTR in silico serotyping tool title_md: sistr_cmd - - description_md: '
  • Galaxy tool ids: smgu_frameshift_deletions_checks
  • Description: - Set of utilities for manipulating small viral genome data.
  • bio.tool - id: v-pipe
  • bio.tool ids: v-pipe
  • biii: - nan
  • bio.tool name: V-pipe
  • bio.tool description: - Bioinformatics pipeline for the analysis of next-generation sequencing data - derived from intra-host viral populations.
  • EDAM operation: - Read pre-processing, Sequence alignment, Genetic variation analysis
  • EDAM - topic: Genomics, Population genetics, Workflows, Virology, Sequencing
  • Status: - Up-to-date
  • Source: https://github.com/cbg-ethz/smallgenomeutilities
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: smallgenomeutilities
  • Date - of first commit of the suite: 2023-05-30
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities
  • Galaxy - wrapper version: 0.4.1
  • Conda id: smallgenomeutilities
  • Conda - version: 0.4.1
  • EDAM operation (no superclasses): - Read pre-processing, Sequence alignment, Genetic variation analysis
  • EDAM - topic (no superclasses): Genomics, Population genetics, Workflows, Virology, - Sequencing
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 158
  • No. of tool - users (all time) (usegalaxy.eu): 158
  • Tool usage (5 years) - (usegalaxy.eu): 8
  • Tool usage (all time) (usegalaxy.eu): - 8
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 158
  • No. - of tool users (all time) - all main servers: 158
  • Tool usage - (5 years) - all main servers: 8
  • Tool usage (all time) - - all main servers: 8
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Set of utilities for manipulating small viral genome data. title_md: smallgenomeutilities - - description_md: '
  • Galaxy tool ids: smalt
  • Description: - SMALT aligns DNA sequencing reads with a reference genome.
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: Up-to-date
  • Source: http://www.sanger.ac.uk/science/tools/smalt-0
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: smalt
  • Date - of first commit of the suite: 2017-09-19
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://sourceforge.net/projects/smalt/
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt
  • Galaxy - wrapper version: 0.7.6
  • Conda id: smalt
  • Conda - version: 0.7.6
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: SMALT aligns DNA sequencing reads with a reference genome. title_md: smalt - - description_md: '
  • Galaxy tool ids: snap, snap_training
  • Description: - SNAP is a general purpose gene finding program suitable for both eukaryotic - and prokaryotic genomes.
  • bio.tool id: snap
  • bio.tool - ids: snap
  • biii: nan
  • bio.tool name: - SNAP
  • bio.tool description: The Semi-HMM-based Nucleic Acid - Parser is a gene prediction tool.
  • EDAM operation: Gene - prediction
  • EDAM topic: DNA, DNA polymorphism, Genetics
  • Status: - Up-to-date
  • Source: https://github.com/KorfLab/SNAP
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: snap
  • Date - of first commit of the suite: 2017-10-12
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap
  • Galaxy - wrapper version: 2013_11_29
  • Conda id: snap
  • Conda - version: 2013_11_29
  • EDAM operation (no superclasses): - Gene prediction
  • EDAM topic (no superclasses): DNA polymorphism, - Genetics
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1499
  • No. of tool - users (all time) (usegalaxy.eu): 1638
  • Tool usage (5 years) - (usegalaxy.eu): 331
  • Tool usage (all time) (usegalaxy.eu): - 358
  • No. of tool users (5 years) (usegalaxy.org): 779
  • No. - of tool users (all time) (usegalaxy.org): 779
  • Tool usage - (5 years) (usegalaxy.org): 244
  • Tool usage (all time) (usegalaxy.org): - 244
  • No. of tool users (5 years) (usegalaxy.org.au): 467
  • No. - of tool users (all time) (usegalaxy.org.au): 467
  • Tool usage - (5 years) (usegalaxy.org.au): 83
  • Tool usage (all time) - (usegalaxy.org.au): 83
  • No. of tool users (5 years) - all - main servers: 2745
  • No. of tool users (all time) - all main - servers: 2884
  • Tool usage (5 years) - all main servers: - 658
  • Tool usage (all time) - all main servers: 685
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: SNAP is a general purpose gene finding program suitable for both + eukaryotic and prokaryotic genomes. title_md: snap - - description_md: '
  • Galaxy tool ids: snippy_core, snippy, snippy_clean_full_aln
  • Description: - Contains the snippy tool for characterising microbial snps
  • bio.tool - id: snippy
  • bio.tool ids: snippy
  • biii: - nan
  • bio.tool name: snippy
  • bio.tool description: - Rapid haploid variant calling and core SNP phylogeny generation.
  • EDAM - operation: Phylogenetic tree visualisation, Phylogenetic tree generation, - Variant calling
  • EDAM topic: Genomics, Model organisms, - DNA polymorphism, Phylogenetics
  • Status: To update
  • Source: - https://github.com/tseemann/snippy
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: snippy
  • Date - of first commit of the suite: 2019-04-02
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy
  • Galaxy - wrapper version: nan
  • Conda id: snippy
  • Conda - version: 4.6.0
  • EDAM operation (no superclasses): - Phylogenetic tree visualisation, Variant calling
  • EDAM topic (no - superclasses): Genomics, Model organisms, DNA polymorphism, Phylogenetics
  • Available - on UseGalaxy.org (Main): 3
  • Available on UseGalaxy.org.au: - 3
  • Available on UseGalaxy.eu: 3
  • Available - on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): - 3
  • Tools available on UseGalaxy.org.au: 3
  • Tools - available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: - 3
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 2
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 121363
  • No. of tool - users (all time) (usegalaxy.eu): 124773
  • Tool usage (5 years) - (usegalaxy.eu): 3448
  • Tool usage (all time) (usegalaxy.eu): - 3602
  • No. of tool users (5 years) (usegalaxy.org): 92504
  • No. - of tool users (all time) (usegalaxy.org): 92504
  • Tool usage - (5 years) (usegalaxy.org): 3945
  • Tool usage (all time) (usegalaxy.org): - 3945
  • No. of tool users (5 years) (usegalaxy.org.au): 48068
  • No. - of tool users (all time) (usegalaxy.org.au): 52034
  • Tool - usage (5 years) (usegalaxy.org.au): 2705
  • Tool usage (all - time) (usegalaxy.org.au): 3073
  • No. of tool users (5 years) - - all main servers: 261935
  • No. of tool users (all time) - - all main servers: 269311
  • Tool usage (5 years) - all main - servers: 10098
  • Tool usage (all time) - all main servers: - 10620
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Contains the snippy tool for characterising microbial snps title_md: snippy - - description_md: '
  • Galaxy tool ids: sonneityping
  • Description: - Scripts for parsing Mykrobe predict results for Shigella sonnei.
  • bio.tool - id: sonneityping
  • bio.tool ids: sonneityping
  • biii: - nan
  • bio.tool name: sonneityping
  • bio.tool - description: Scripts for parsing Mykrobe predict results for Shigella - sonnei.
  • EDAM operation: Antimicrobial resistance prediction, - Variant calling, Genotyping
  • EDAM topic: Whole genome sequencing, - Genotype and phenotype, Genetic variation, Metagenomics
  • Status: - Up-to-date
  • Source: https://github.com/katholt/sonneityping
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: sonneityping
  • Date - of first commit of the suite: 2021-09-16
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/katholt/sonneityping
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping
  • Galaxy - wrapper version: 20210201
  • Conda id: sonneityping
  • Conda - version: 20210201
  • EDAM operation (no superclasses): - Antimicrobial resistance prediction, Variant calling, Genotyping
  • EDAM - topic (no superclasses): Whole genome sequencing, Genotype and phenotype, - Genetic variation, Metagenomics
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1
  • No. of tool users (all time) (usegalaxy.eu): 1
  • Tool - usage (5 years) (usegalaxy.eu): 1
  • Tool usage (all time) - (usegalaxy.eu): 1
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 1
  • No. of tool users (all time) - all main - servers: 1
  • Tool usage (5 years) - all main servers: - 1
  • Tool usage (all time) - all main servers: 1
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Scripts for parsing Mykrobe predict results for Shigella sonnei. title_md: sonneityping - - description_md: '
  • Galaxy tool ids: bg_sortmerna
  • Description: - SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from - metatransriptomic data produced by next-generation sequencers.
  • bio.tool - id: sortmerna
  • bio.tool ids: sortmerna
  • biii: - nan
  • bio.tool name: SortMeRNA
  • bio.tool description: - Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
  • EDAM - operation: Sequence similarity search, Sequence comparison, Sequence - alignment analysis
  • EDAM topic: Metatranscriptomics, Metagenomics
  • Status: - To update
  • Source: http://bioinfo.lifl.fr/RNA/sortmerna/
  • ToolShed - categories: RNA
  • ToolShed id: sortmerna
  • Date - of first commit of the suite: 2016-03-17
  • Galaxy wrapper - owner: rnateam
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna
  • Galaxy - wrapper version: 4.3.6
  • Conda id: sortmerna
  • Conda - version: 4.3.7
  • EDAM operation (no superclasses): - Sequence similarity search, Sequence alignment analysis
  • EDAM topic - (no superclasses): Metatranscriptomics, Metagenomics
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 19865
  • No. of tool - users (all time) (usegalaxy.eu): 21034
  • Tool usage (5 years) - (usegalaxy.eu): 1047
  • Tool usage (all time) (usegalaxy.eu): - 1126
  • No. of tool users (5 years) (usegalaxy.org): 3141
  • No. - of tool users (all time) (usegalaxy.org): 3141
  • Tool usage - (5 years) (usegalaxy.org): 328
  • Tool usage (all time) (usegalaxy.org): - 328
  • No. of tool users (5 years) (usegalaxy.org.au): 3304
  • No. - of tool users (all time) (usegalaxy.org.au): 3304
  • Tool - usage (5 years) (usegalaxy.org.au): 189
  • Tool usage (all - time) (usegalaxy.org.au): 189
  • No. of tool users (5 years) - - all main servers: 26310
  • No. of tool users (all time) - - all main servers: 27479
  • Tool usage (5 years) - all main - servers: 1564
  • Tool usage (all time) - all main servers: - 1643
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: SortMeRNA is a software designed to rapidly filter ribosomal RNA + fragments from metatransriptomic data produced by next-generation sequencers. title_md: sortmerna - - description_md: "
  • Galaxy tool ids: spades_biosyntheticspades,\ - \ spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades,\ - \ spades_plasmidspades, rnaspades, spades_rnaviralspades, spades
  • 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.
  • bio.tool id:\ - \ spades
  • bio.tool ids: plasmidspades, metaplasmidspades,\ - \ rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades,\ - \ rnaviralspades
  • biii: nan
  • bio.tool name:\ - \ SPAdes
  • 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.
  • EDAM\ - \ operation: Genome assembly
  • EDAM topic: Sequence\ - \ assembly
  • Status: To update
  • Source:\ - \ https://github.com/ablab/spades
  • ToolShed categories:\ - \ Assembly, RNA, Metagenomics
  • ToolShed id: spades
  • Date\ - \ of first commit of the suite: 2017-06-30
  • Galaxy wrapper\ - \ owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades
  • Galaxy\ - \ wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades
  • Galaxy\ - \ wrapper version: 3.15.5
  • Conda id: spades
  • Conda\ - \ version: 4.0.0
  • EDAM operation (no superclasses):\ - \ Genome assembly
  • EDAM topic (no superclasses): Sequence\ - \ assembly
  • Available on UseGalaxy.org (Main): 9
  • Available\ - \ on UseGalaxy.org.au: 9
  • Available on UseGalaxy.eu:\ - \ 9
  • Available on UseGalaxy.fr: 9
  • Tools available\ - \ on UseGalaxy.org (Main): 9
  • Tools available on UseGalaxy.org.au:\ - \ 9
  • Tools available on UseGalaxy.eu: 9
  • Tools\ - \ available on UseGalaxy.fr: 9
  • Tools available on APOSTL:\ - \ 0
  • Tools available on ARGs-OAP: 0
  • Tools\ - \ available on CIRM-CFBP: 0
  • Tools available on ChemFlow:\ - \ 0
  • Tools available 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.no: 3
  • Tools\ - \ available on Viral Variant Visualizer (VVV): 0
  • No. of\ - \ tool users (5 years) (usegalaxy.eu): 82716
  • No. of tool\ - \ users (all time) (usegalaxy.eu): 87113
  • Tool usage (5\ - \ years) (usegalaxy.eu): 8209
  • Tool usage (all time) (usegalaxy.eu):\ - \ 8526
  • No. of tool users (5 years) (usegalaxy.org): 120471
  • No.\ - \ of tool users (all time) (usegalaxy.org): 120475
  • Tool\ - \ usage (5 years) (usegalaxy.org): 14787
  • Tool usage (all\ - \ time) (usegalaxy.org): 14790
  • No. of tool users (5 years)\ - \ (usegalaxy.org.au): 54067
  • No. of tool users (all time)\ - \ (usegalaxy.org.au): 61541
  • Tool usage (5 years) (usegalaxy.org.au):\ - \ 5817
  • Tool usage (all time) (usegalaxy.org.au): 6653
  • No.\ - \ of tool users (5 years) - all main servers: 257254
  • No.\ - \ of tool users (all time) - all main servers: 269129
  • Tool\ - \ usage (5 years) - all main servers: 28813
  • Tool usage\ - \ (all time) - all main servers: 29969
  • Reviewed:\ - \ True
  • To keep: True
  • Deprecated: False
" + - description_md: '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.' title_md: spades - - description_md: '
  • Galaxy tool ids: spotyping
  • Description: - SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from - sequence reads
  • bio.tool id: spotyping
  • bio.tool - ids: spotyping
  • biii: nan
  • bio.tool - name: SpoTyping
  • bio.tool description: Fast and accurate - in silico Mycobacterium spoligotyping from sequence reads.
  • EDAM - operation: Variant pattern analysis
  • EDAM topic: - Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic - variation
  • Status: Up-to-date
  • Source: - https://github.com/xiaeryu/SpoTyping-v2.0
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: spotyping
  • Date - of first commit of the suite: 2018-05-07
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping
  • Galaxy - wrapper version: 2.1
  • Conda id: spotyping
  • Conda - version: 2.1
  • EDAM operation (no superclasses): Variant - pattern analysis
  • EDAM topic (no superclasses): Microbiology, - Sequencing, Sequence composition, complexity and repeats, Genetic variation
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 1436
  • No. of tool - users (all time) (usegalaxy.eu): 1436
  • Tool usage (5 years) - (usegalaxy.eu): 23
  • Tool usage (all time) (usegalaxy.eu): - 23
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1436
  • No. - of tool users (all time) - all main servers: 1436
  • Tool - usage (5 years) - all main servers: 23
  • Tool usage (all - time) - all main servers: 23
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping + from sequence reads title_md: spotyping - - description_md: '
  • Galaxy tool ids: bowtieForSmallRNA
  • Description: - bowtie wrapper tool to align small RNA sequencing reads
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: http://artbio.fr
  • ToolShed - categories: RNA, Next Gen Mappers
  • ToolShed id: sr_bowtie
  • Date - of first commit of the suite: 2017-09-02
  • Galaxy wrapper - owner: artbio
  • Galaxy wrapper source: https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie
  • Galaxy - wrapper parsed folder: https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie
  • Galaxy - wrapper version: 2.3.0
  • Conda id: bowtie
  • Conda - version: 1.3.1
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available 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: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 80
  • No. of tool - users (all time) (usegalaxy.org): 80
  • Tool usage (5 years) - (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): - 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 80
  • No. - of tool users (all time) - all main servers: 80
  • Tool usage - (5 years) - all main servers: 1
  • Tool usage (all time) - - all main servers: 1
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: bowtie wrapper tool to align small RNA sequencing reads title_md: sr_bowtie - - description_md: '
  • Galaxy tool ids: srst2
  • Description: - Short Read Sequence Typing for Bacterial Pathogens
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: nan
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: srst2
  • Date - of first commit of the suite: 2015-12-02
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: nan
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2
  • Galaxy - wrapper version: 0.3.7
  • Conda id: srst2
  • Conda - version: 0.2.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 297
  • No. of tool - users (all time) (usegalaxy.eu): 297
  • Tool usage (5 years) - (usegalaxy.eu): 40
  • Tool usage (all time) (usegalaxy.eu): - 40
  • No. of tool users (5 years) (usegalaxy.org): 71
  • No. - of tool users (all time) (usegalaxy.org): 71
  • Tool usage - (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): - 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 368
  • No. - of tool users (all time) - all main servers: 368
  • Tool usage - (5 years) - all main servers: 41
  • Tool usage (all time) - - all main servers: 41
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Short Read Sequence Typing for Bacterial Pathogens title_md: srst2 - - description_md: '
  • Galaxy tool ids: srst2
  • Description: - SRST2 Short Read Sequence Typing for Bacterial Pathogens
  • bio.tool - id: srst2
  • bio.tool ids: srst2
  • biii: - nan
  • bio.tool name: srst2
  • bio.tool description: - Short Read Sequence Typing for Bacterial Pathogens
  • EDAM operation: - Multilocus sequence typing
  • EDAM topic: Whole genome sequencing, - Public health and epidemiology
  • Status: To update
  • Source: - http://katholt.github.io/srst2/
  • ToolShed categories: Metagenomics
  • ToolShed - id: srst2
  • Date of first commit of the suite: 2022-08-22
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/katholt/srst2
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2
  • Galaxy - wrapper version: 0.2.0
  • Conda id: samtools
  • Conda - version: 1.21
  • EDAM operation (no superclasses): - Multilocus sequence typing
  • EDAM topic (no superclasses): - Whole genome sequencing, Public health and epidemiology
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 297
  • No. of tool - users (all time) (usegalaxy.eu): 297
  • Tool usage (5 years) - (usegalaxy.eu): 40
  • Tool usage (all time) (usegalaxy.eu): - 40
  • No. of tool users (5 years) (usegalaxy.org): 71
  • No. - of tool users (all time) (usegalaxy.org): 71
  • Tool usage - (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): - 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 368
  • No. - of tool users (all time) - all main servers: 368
  • Tool usage - (5 years) - all main servers: 41
  • Tool usage (all time) - - all main servers: 41
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: SRST2 Short Read Sequence Typing for Bacterial Pathogens title_md: srst2 - - description_md: '
  • Galaxy tool ids: staramr_search
  • Description: - Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial - resistance databases.
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: - https://github.com/phac-nml/staramr
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: staramr
  • Date - of first commit of the suite: 2022-06-10
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr
  • Galaxy - wrapper version: 0.10.0
  • Conda id: staramr
  • Conda - version: 0.10.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 20778
  • No. of tool - users (all time) (usegalaxy.eu): 20891
  • Tool usage (5 years) - (usegalaxy.eu): 2030
  • Tool usage (all time) (usegalaxy.eu): - 2045
  • No. of tool users (5 years) (usegalaxy.org): 9520
  • No. - of tool users (all time) (usegalaxy.org): 9520
  • Tool usage - (5 years) (usegalaxy.org): 1424
  • Tool usage (all time) (usegalaxy.org): - 1424
  • No. of tool users (5 years) (usegalaxy.org.au): 6753
  • No. - of tool users (all time) (usegalaxy.org.au): 6753
  • Tool - usage (5 years) (usegalaxy.org.au): 864
  • Tool usage (all - time) (usegalaxy.org.au): 864
  • No. of tool users (5 years) - - all main servers: 37051
  • No. of tool users (all time) - - all main servers: 37164
  • Tool usage (5 years) - all main - servers: 4318
  • Tool usage (all time) - all main servers: - 4333
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Scan genome contigs against the ResFinder, PlasmidFinder, and + PointFinder antimicrobial resistance databases. title_md: staramr - - description_md: '
  • Galaxy tool ids: stringmlst
  • Description: - Rapid and accurate identification of the sequence type (ST)
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: nan
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: stringmlst
  • Date - of first commit of the suite: 2016-10-19
  • Galaxy wrapper - owner: nml
  • Galaxy wrapper source: nan
  • Galaxy - wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst
  • Galaxy - wrapper version: 1.1.0
  • Conda id: stringMLST
  • Conda - version: 0.6.3
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 0
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 0
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
  • Tool usage (5 years) (usegalaxy.eu): - 0
  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
  • No. of tool - users (all time) (usegalaxy.org): 0
  • Tool usage (5 years) - (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Rapid and accurate identification of the sequence type (ST) title_md: stringmlst - - description_md: '
  • Galaxy tool ids: structure
  • Description: - for using multi-locus genotype data to investigate population structure.
  • bio.tool - id: structure
  • bio.tool ids: structure
  • biii: - nan
  • bio.tool name: Structure
  • 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.
  • EDAM - operation: Genetic variation analysis
  • EDAM topic: - Population genetics
  • Status: Up-to-date
  • Source: - https://web.stanford.edu/group/pritchardlab/structure.html
  • ToolShed - categories: Phylogenetics, Variant Analysis
  • ToolShed id: - structure
  • Date of first commit of the suite: 2017-09-22
  • Galaxy - wrapper owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure
  • Galaxy - wrapper version: 2.3.4
  • Conda id: structure
  • Conda - version: 2.3.4
  • EDAM operation (no superclasses): - Genetic variation analysis
  • EDAM topic (no superclasses): - Population genetics
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 2858
  • No. of tool users (all time) (usegalaxy.eu): 3001
  • Tool - usage (5 years) (usegalaxy.eu): 118
  • Tool usage (all time) - (usegalaxy.eu): 123
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
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  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 2858
  • No. of tool users (all time) - all main - servers: 3001
  • Tool usage (5 years) - all main servers: - 118
  • Tool usage (all time) - all main servers: 123
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: for using multi-locus genotype data to investigate population + structure. title_md: structure - - description_md: '
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  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool - description: nan
  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - https://github.com/qiime2/q2-alignment
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: - nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 3
  • Available - on UseGalaxy.org.au: 3
  • Available on UseGalaxy.eu: - 3
  • Available on UseGalaxy.fr: 3
  • Tools available - on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: - 3
  • Tools available on UseGalaxy.eu: 3
  • Tools - available on UseGalaxy.fr: 3
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 249
  • No. of tool - users (all time) (usegalaxy.eu): 249
  • Tool usage (5 years) - (usegalaxy.eu): 32
  • Tool usage (all time) (usegalaxy.eu): - 32
  • No. of tool users (5 years) (usegalaxy.org): 16
  • No. - of tool users (all time) (usegalaxy.org): 16
  • Tool usage - (5 years) (usegalaxy.org): 10
  • Tool usage (all time) (usegalaxy.org): - 10
  • No. of tool users (5 years) (usegalaxy.org.au): 102
  • No. - of tool users (all time) (usegalaxy.org.au): 102
  • Tool usage - (5 years) (usegalaxy.org.au): 16
  • Tool usage (all time) - (usegalaxy.org.au): 16
  • No. of tool users (5 years) - all - main servers: 367
  • No. of tool users (all time) - all main - servers: 367
  • Tool usage (5 years) - all main servers: - 58
  • Tool usage (all time) - all main servers: 58
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__alignment - - description_md: '
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  • Description: nan
  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
  • bio.tool description: - nan
  • EDAM operation: nan
  • EDAM topic: - nan
  • Status: To update
  • Source: https://github.com/qiime2/q2-composition
  • ToolShed - categories: Metagenomics, Sequence Analysis, Statistics
  • ToolShed - id: nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 4
  • Available - on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: - 4
  • Available on UseGalaxy.fr: 2
  • Tools available - on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: - 4
  • Tools available on UseGalaxy.eu: 4
  • Tools - available on UseGalaxy.fr: 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 117
  • No. of tool - users (all time) (usegalaxy.eu): 117
  • Tool usage (5 years) - (usegalaxy.eu): 41
  • Tool usage (all time) (usegalaxy.eu): - 41
  • No. of tool users (5 years) (usegalaxy.org): 84
  • No. - of tool users (all time) (usegalaxy.org): 84
  • Tool usage - (5 years) (usegalaxy.org): 24
  • Tool usage (all time) (usegalaxy.org): - 24
  • No. of tool users (5 years) (usegalaxy.org.au): 161
  • No. - of tool users (all time) (usegalaxy.org.au): 161
  • Tool usage - (5 years) (usegalaxy.org.au): 13
  • Tool usage (all time) - (usegalaxy.org.au): 13
  • No. of tool users (5 years) - all - main servers: 362
  • No. of tool users (all time) - all main - servers: 362
  • Tool usage (5 years) - all main servers: - 78
  • Tool usage (all time) - all main servers: 78
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__composition - - description_md: '
  • Galaxy tool ids: qiime2__cutadapt__demux_paired, - qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single
  • Description: - nan
  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool - description: nan
  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - https://github.com/qiime2/q2-cutadapt
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: - nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 4
  • Available - on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: - 4
  • Available on UseGalaxy.fr: 4
  • Tools available - on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: - 4
  • Tools available on UseGalaxy.eu: 4
  • Tools - available on UseGalaxy.fr: 4
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 217
  • No. of tool - users (all time) (usegalaxy.eu): 217
  • Tool usage (5 years) - (usegalaxy.eu): 47
  • Tool usage (all time) (usegalaxy.eu): - 47
  • No. of tool users (5 years) (usegalaxy.org): 42
  • No. - of tool users (all time) (usegalaxy.org): 42
  • Tool usage - (5 years) (usegalaxy.org): 20
  • Tool usage (all time) (usegalaxy.org): - 20
  • No. of tool users (5 years) (usegalaxy.org.au): 96
  • No. - of tool users (all time) (usegalaxy.org.au): 96
  • Tool usage - (5 years) (usegalaxy.org.au): 12
  • Tool usage (all time) - (usegalaxy.org.au): 12
  • No. of tool users (5 years) - all - main servers: 355
  • No. of tool users (all time) - all main - servers: 355
  • Tool usage (5 years) - all main servers: - 79
  • Tool usage (all time) - all main servers: 79
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__cutadapt - - description_md: '
  • Galaxy tool ids: qiime2__dada2__denoise_ccs, - qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single
  • Description: - nan
  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
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  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - http://benjjneb.github.io/dada2/
  • ToolShed categories: Metagenomics, - Sequence Analysis, Statistics
  • ToolShed id: nan
  • Date - of first commit of the suite: 2022-08-26
  • Galaxy wrapper - owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 4
  • Available - on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: - 4
  • Available on UseGalaxy.fr: 4
  • Tools available - on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: - 4
  • Tools available on UseGalaxy.eu: 4
  • Tools - available on UseGalaxy.fr: 4
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
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  • No. of tool - users (all time) (usegalaxy.eu): 721
  • Tool usage (5 years) - (usegalaxy.eu): 160
  • Tool usage (all time) (usegalaxy.eu): - 160
  • No. of tool users (5 years) (usegalaxy.org): 350
  • No. - of tool users (all time) (usegalaxy.org): 350
  • Tool usage - (5 years) (usegalaxy.org): 91
  • Tool usage (all time) (usegalaxy.org): - 91
  • No. of tool users (5 years) (usegalaxy.org.au): 214
  • No. - of tool users (all time) (usegalaxy.org.au): 214
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  • Tool usage (all time) - (usegalaxy.org.au): 35
  • No. of tool users (5 years) - all - main servers: 1285
  • No. of tool users (all time) - all main - servers: 1285
  • Tool usage (5 years) - all main servers: - 286
  • Tool usage (all time) - all main servers: 286
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__dada2 - - description_md: '
  • Galaxy tool ids: qiime2__deblur__denoise_16S, - qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats
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  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
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  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - https://github.com/biocore/deblur
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: - nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 3
  • Available - on UseGalaxy.org.au: 3
  • Available on UseGalaxy.eu: - 3
  • Available on UseGalaxy.fr: 3
  • Tools available - on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: - 3
  • Tools available on UseGalaxy.eu: 3
  • Tools - available on UseGalaxy.fr: 3
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
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  • No. of tool - users (all time) (usegalaxy.eu): 125
  • Tool usage (5 years) - (usegalaxy.eu): 30
  • Tool usage (all time) (usegalaxy.eu): - 30
  • No. of tool users (5 years) (usegalaxy.org): 13
  • No. - of tool users (all time) (usegalaxy.org): 13
  • Tool usage - (5 years) (usegalaxy.org): 9
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  • No. of tool users (5 years) (usegalaxy.org.au): 83
  • No. - of tool users (all time) (usegalaxy.org.au): 83
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  • Tool usage (all time) (usegalaxy.org.au): - 8
  • No. of tool users (5 years) - all main servers: 221
  • No. - of tool users (all time) - all main servers: 221
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  • Tool usage (all time) - - all main servers: 47
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__deblur - - description_md: '
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  • bio.tool ids: - nan
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  • EDAM - topic: nan
  • Status: To update
  • Source: - https://github.com/qiime2/q2-demux
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: - nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 6
  • Available - on UseGalaxy.org.au: 6
  • Available on UseGalaxy.eu: - 6
  • Available on UseGalaxy.fr: 6
  • Tools available - on UseGalaxy.org (Main): 6
  • Tools available on UseGalaxy.org.au: - 6
  • Tools available on UseGalaxy.eu: 6
  • Tools - available on UseGalaxy.fr: 6
  • Tools available on APOSTL: - 0
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  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
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  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
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  • Tools available on HyPhy HIV - NGS Tools: 0
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  • Tools available on Viral Variant Visualizer (VVV): 0
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  • No. of tool - users (all time) (usegalaxy.eu): 396
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  • Tool usage (all time) (usegalaxy.eu): - 134
  • No. of tool users (5 years) (usegalaxy.org): 121
  • No. - of tool users (all time) (usegalaxy.org): 121
  • Tool usage - (5 years) (usegalaxy.org): 57
  • Tool usage (all time) (usegalaxy.org): - 57
  • No. of tool users (5 years) (usegalaxy.org.au): 144
  • No. - of tool users (all time) (usegalaxy.org.au): 144
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  • Tool usage (all time) - (usegalaxy.org.au): 39
  • No. of tool users (5 years) - all - main servers: 661
  • No. of tool users (all time) - all main - servers: 661
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  • Tool usage (all time) - all main servers: 230
  • Reviewed: - True
  • To keep: True
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  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
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  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
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  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib
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  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor
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  • Reviewed: - True
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  • No. of tool users (5 years) (usegalaxy.org): 9
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  • Tool usage - (5 years) (usegalaxy.org): 5
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  • No. of tool users (5 years) (usegalaxy.org.au): 0
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  • No. of tool users (5 years) - all main servers: 55
  • No. - of tool users (all time) - all main servers: 55
  • Tool usage - (5 years) - all main servers: 18
  • Tool usage (all time) - - all main servers: 18
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
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  • bio.tool - id: nan
  • bio.tool ids: nan
  • biii: - nan
  • bio.tool name: nan
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  • EDAM operation: nan
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  • Status: To update
  • Source: https://github.com/qiime2/q2-longitudinal
  • ToolShed - categories: Metagenomics, Sequence Analysis, Statistics
  • ToolShed - id: nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
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  • EDAM operation (no - superclasses): nan
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  • Available on UseGalaxy.org (Main): 11
  • Available - on UseGalaxy.org.au: 11
  • Available on UseGalaxy.eu: - 11
  • Available on UseGalaxy.fr: 11
  • Tools available - on UseGalaxy.org (Main): 11
  • Tools available on UseGalaxy.org.au: - 11
  • Tools available on UseGalaxy.eu: 11
  • Tools - available on UseGalaxy.fr: 11
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
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  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 11
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
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  • No. of tool - users (all time) (usegalaxy.eu): 37
  • Tool usage (5 years) - (usegalaxy.eu): 16
  • Tool usage (all time) (usegalaxy.eu): - 16
  • No. of tool users (5 years) (usegalaxy.org): 22
  • No. - of tool users (all time) (usegalaxy.org): 22
  • Tool usage - (5 years) (usegalaxy.org): 7
  • Tool usage (all time) (usegalaxy.org): - 7
  • No. of tool users (5 years) (usegalaxy.org.au): 89
  • No. - of tool users (all time) (usegalaxy.org.au): 89
  • Tool usage - (5 years) (usegalaxy.org.au): 14
  • Tool usage (all time) - (usegalaxy.org.au): 14
  • No. of tool users (5 years) - all - main servers: 148
  • No. of tool users (all time) - all main - servers: 148
  • Tool usage (5 years) - all main servers: - 37
  • Tool usage (all time) - all main servers: 37
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
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  • Status: To update
  • Source: - https://github.com/qiime2/q2-metadata
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: - nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
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  • EDAM operation (no - superclasses): nan
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  • Available on UseGalaxy.org (Main): 3
  • Available - on UseGalaxy.org.au: 3
  • Available on UseGalaxy.eu: - 3
  • Available on UseGalaxy.fr: 3
  • Tools available - on UseGalaxy.org (Main): 3
  • Tools available on UseGalaxy.org.au: - 3
  • Tools available on UseGalaxy.eu: 3
  • Tools - available on UseGalaxy.fr: 3
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
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  • Tools available on Palfinder: 0
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  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 3
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
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  • No. of tool - users (all time) (usegalaxy.eu): 615
  • Tool usage (5 years) - (usegalaxy.eu): 143
  • Tool usage (all time) (usegalaxy.eu): - 143
  • No. of tool users (5 years) (usegalaxy.org): 246
  • No. - of tool users (all time) (usegalaxy.org): 246
  • Tool usage - (5 years) (usegalaxy.org): 75
  • Tool usage (all time) (usegalaxy.org): - 75
  • No. of tool users (5 years) (usegalaxy.org.au): 115
  • No. - of tool users (all time) (usegalaxy.org.au): 115
  • Tool usage - (5 years) (usegalaxy.org.au): 27
  • Tool usage (all time) - (usegalaxy.org.au): 27
  • No. of tool users (5 years) - all - main servers: 976
  • No. of tool users (all time) - all main - servers: 976
  • Tool usage (5 years) - all main servers: - 245
  • Tool usage (all time) - all main servers: 245
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
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  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool - description: nan
  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - https://github.com/qiime2/q2-phylogeny
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: - nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
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  • EDAM operation (no - superclasses): nan
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  • Available on UseGalaxy.org (Main): 12
  • Available - on UseGalaxy.org.au: 12
  • Available on UseGalaxy.eu: - 12
  • Available on UseGalaxy.fr: 12
  • Tools available - on UseGalaxy.org (Main): 12
  • Tools available on UseGalaxy.org.au: - 12
  • Tools available on UseGalaxy.eu: 12
  • Tools - available on UseGalaxy.fr: 12
  • Tools available on APOSTL: - 0
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  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
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  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 12
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  • Tools available on Viral Variant Visualizer (VVV): 0
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  • No. of tool - users (all time) (usegalaxy.eu): 330
  • Tool usage (5 years) - (usegalaxy.eu): 83
  • Tool usage (all time) (usegalaxy.eu): - 83
  • No. of tool users (5 years) (usegalaxy.org): 64
  • No. - of tool users (all time) (usegalaxy.org): 64
  • Tool usage - (5 years) (usegalaxy.org): 40
  • Tool usage (all time) (usegalaxy.org): - 40
  • No. of tool users (5 years) (usegalaxy.org.au): 195
  • No. - of tool users (all time) (usegalaxy.org.au): 195
  • Tool usage - (5 years) (usegalaxy.org.au): 49
  • Tool usage (all time) - (usegalaxy.org.au): 49
  • No. of tool users (5 years) - all - main servers: 589
  • No. of tool users (all time) - all main - servers: 589
  • Tool usage (5 years) - all main servers: - 172
  • Tool usage (all time) - all main servers: 172
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__phylogeny - - description_md: '
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  • bio.tool ids: nan
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  • Status: To update
  • Source: https://github.com/qiime2/q2-quality-control
  • ToolShed - categories: Metagenomics, Sequence Analysis, Statistics
  • ToolShed - id: nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
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  • EDAM operation (no - superclasses): nan
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  • Available on UseGalaxy.org (Main): 6
  • Available - on UseGalaxy.org.au: 6
  • Available on UseGalaxy.eu: - 6
  • Available on UseGalaxy.fr: 6
  • Tools available - on UseGalaxy.org (Main): 6
  • Tools available on UseGalaxy.org.au: - 6
  • Tools available on UseGalaxy.eu: 6
  • Tools - available on UseGalaxy.fr: 6
  • Tools available on APOSTL: - 0
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  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
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  • Tools available on Galaxy@AuBi: 0
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  • Tools available on HyPhy HIV - NGS Tools: 0
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  • No. - of tool users (5 years) (usegalaxy.eu): 4
  • No. of tool users - (all time) (usegalaxy.eu): 4
  • Tool usage (5 years) (usegalaxy.eu): - 4
  • Tool usage (all time) (usegalaxy.eu): 4
  • No. - of tool users (5 years) (usegalaxy.org): 5
  • No. of tool - users (all time) (usegalaxy.org): 5
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  • Tool usage (all time) (usegalaxy.org): - 5
  • No. of tool users (5 years) (usegalaxy.org.au): 1
  • No. - of tool users (all time) (usegalaxy.org.au): 1
  • Tool usage - (5 years) (usegalaxy.org.au): 1
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  • No. of tool users (5 years) - all main servers: 10
  • No. - of tool users (all time) - all main servers: 10
  • Tool usage - (5 years) - all main servers: 10
  • Tool usage (all time) - - all main servers: 10
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__quality_control - - description_md: '
  • Galaxy tool ids: qiime2__quality_filter__q_score
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  • Source: - https://github.com/qiime2/q2-quality-filter
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
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  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
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  • EDAM operation (no - superclasses): nan
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  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 1
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 1
  • Tools available on APOSTL: - 0
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  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
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  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
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  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
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  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
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  • Tools available on PhagePromotor: - 0
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  • Tools available on Viral Variant Visualizer (VVV): 0
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  • No. of tool - users (all time) (usegalaxy.eu): 29
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  • No. of tool users (5 years) (usegalaxy.org): 16
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  • No. of tool users (5 years) (usegalaxy.org.au): 37
  • No. - of tool users (all time) (usegalaxy.org.au): 37
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  • No. of tool users (5 years) - all main servers: 82
  • No. - of tool users (all time) - all main servers: 82
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  • Tool usage (all time) - - all main servers: 22
  • Reviewed: True
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  • Status: To update
  • Source: - https://github.com/nbokulich/RESCRIPt
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
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  • Date of first commit of the suite: 2024-04-25
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
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  • Tools available - on UseGalaxy.org (Main): 0
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  • Tools available on APOSTL: - 0
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  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 0
  • No. of tool users - (all time) (usegalaxy.eu): 0
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  • Tool usage (all time) (usegalaxy.eu): 0
  • No. - of tool users (5 years) (usegalaxy.org): 0
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  • No. of tool users (5 years) (usegalaxy.org.au): 0
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  • Tool usage - (5 years) (usegalaxy.org.au): 0
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  • No. of tool users (5 years) - all main servers: 0
  • No. - of tool users (all time) - all main servers: 0
  • Tool usage - (5 years) - all main servers: 0
  • Tool usage (all time) - - all main servers: 0
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
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  • Description: - nan
  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool - description: nan
  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - https://github.com/qiime2/q2-sample-classifier
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: - nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 15
  • Available - on UseGalaxy.org.au: 15
  • Available on UseGalaxy.eu: - 15
  • Available on UseGalaxy.fr: 15
  • Tools available - on UseGalaxy.org (Main): 15
  • Tools available on UseGalaxy.org.au: - 15
  • Tools available on UseGalaxy.eu: 15
  • Tools - available on UseGalaxy.fr: 15
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 15
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 10
  • No. of tool - users (all time) (usegalaxy.eu): 10
  • Tool usage (5 years) - (usegalaxy.eu): 3
  • Tool usage (all time) (usegalaxy.eu): - 3
  • No. of tool users (5 years) (usegalaxy.org): 14
  • No. - of tool users (all time) (usegalaxy.org): 14
  • Tool usage - (5 years) (usegalaxy.org): 10
  • Tool usage (all time) (usegalaxy.org): - 10
  • No. of tool users (5 years) (usegalaxy.org.au): 5
  • No. - of tool users (all time) (usegalaxy.org.au): 5
  • Tool usage - (5 years) (usegalaxy.org.au): 5
  • Tool usage (all time) (usegalaxy.org.au): - 5
  • No. of tool users (5 years) - all main servers: 29
  • No. - of tool users (all time) - all main servers: 29
  • Tool usage - (5 years) - all main servers: 18
  • Tool usage (all time) - - all main servers: 18
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__sample_classifier - - description_md: '
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  • Description: - nan
  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool - description: nan
  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - https://github.com/qiime2/q2-taxa
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: - nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 4
  • Available - on UseGalaxy.org.au: 4
  • Available on UseGalaxy.eu: - 4
  • Available on UseGalaxy.fr: 4
  • Tools available - on UseGalaxy.org (Main): 4
  • Tools available on UseGalaxy.org.au: - 4
  • Tools available on UseGalaxy.eu: 4
  • Tools - available on UseGalaxy.fr: 4
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 664
  • No. of tool - users (all time) (usegalaxy.eu): 664
  • Tool usage (5 years) - (usegalaxy.eu): 145
  • Tool usage (all time) (usegalaxy.eu): - 145
  • No. of tool users (5 years) (usegalaxy.org): 113
  • No. - of tool users (all time) (usegalaxy.org): 113
  • Tool usage - (5 years) (usegalaxy.org): 43
  • Tool usage (all time) (usegalaxy.org): - 43
  • No. of tool users (5 years) (usegalaxy.org.au): 255
  • No. - of tool users (all time) (usegalaxy.org.au): 255
  • Tool usage - (5 years) (usegalaxy.org.au): 50
  • Tool usage (all time) - (usegalaxy.org.au): 50
  • No. of tool users (5 years) - all - main servers: 1032
  • No. of tool users (all time) - all main - servers: 1032
  • Tool usage (5 years) - all main servers: - 238
  • Tool usage (all time) - all main servers: 238
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__taxa - - description_md: '
  • Galaxy tool ids: qiime2__vsearch__cluster_features_closed_reference, - qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, - qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, - qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref
  • Description: - nan
  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool - description: nan
  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - https://github.com/qiime2/q2-vsearch
  • ToolShed categories: - Metagenomics, Sequence Analysis, Statistics
  • ToolShed id: - nan
  • Date of first commit of the suite: 2022-08-26
  • Galaxy - wrapper owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch
  • Galaxy - wrapper version: 2024.5.0+q2galaxy.2024.5.0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 8
  • Available - on UseGalaxy.org.au: 8
  • Available on UseGalaxy.eu: - 8
  • Available on UseGalaxy.fr: 7
  • Tools available - on UseGalaxy.org (Main): 8
  • Tools available on UseGalaxy.org.au: - 8
  • Tools available on UseGalaxy.eu: 8
  • Tools - available on UseGalaxy.fr: 7
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 84
  • No. of tool - users (all time) (usegalaxy.eu): 84
  • Tool usage (5 years) - (usegalaxy.eu): 52
  • Tool usage (all time) (usegalaxy.eu): - 52
  • No. of tool users (5 years) (usegalaxy.org): 25
  • No. - of tool users (all time) (usegalaxy.org): 25
  • Tool usage - (5 years) (usegalaxy.org): 16
  • Tool usage (all time) (usegalaxy.org): - 16
  • No. of tool users (5 years) (usegalaxy.org.au): 9
  • No. - of tool users (all time) (usegalaxy.org.au): 9
  • Tool usage - (5 years) (usegalaxy.org.au): 5
  • Tool usage (all time) (usegalaxy.org.au): - 5
  • No. of tool users (5 years) - all main servers: 118
  • No. - of tool users (all time) - all main servers: 118
  • Tool usage - (5 years) - all main servers: 73
  • Tool usage (all time) - - all main servers: 73
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2__vsearch - - description_md: '
  • Galaxy tool ids: nan
  • Description: - nan
  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
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  • EDAM - topic: nan
  • Status: To update
  • Source: - nan
  • ToolShed categories: Statistics, Metagenomics, Sequence - Analysis
  • ToolShed id: nan
  • Date of first commit - of the suite: 2022-08-29
  • Galaxy wrapper owner: q2d2
  • Galaxy - wrapper source: nan
  • Galaxy wrapper parsed folder: - https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core
  • Galaxy - wrapper version: nan
  • Conda id: nan
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 0
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 0
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 0
  • Tools - available on UseGalaxy.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 0
  • No. of tool users (all time) (usegalaxy.eu): 0
  • Tool - usage (5 years) (usegalaxy.eu): 0
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  • No. of tool users (5 years) (usegalaxy.org): - 0
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  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 0
  • No. of tool users (all time) - all main - servers: 0
  • Tool usage (5 years) - all main servers: - 0
  • Tool usage (all time) - all main servers: 0
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: .nan title_md: suite_qiime2_core - - description_md: '
  • Galaxy tool ids: qiime2_core__tools__export, - qiime2_core__tools__import, qiime2_core__tools__import_fastq
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  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool - description: nan
  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - https://qiime2.org
  • ToolShed categories: Metagenomics, Sequence - Analysis, Statistics
  • ToolShed id: nan
  • Date - of first commit of the suite: 2022-08-26
  • Galaxy wrapper - owner: q2d2
  • Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools
  • Galaxy - wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools
  • Galaxy - wrapper version: 2024.5.0+dist.he540b0b0
  • Conda id: - nan
  • Conda version: nan
  • EDAM operation (no - superclasses): nan
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 2
  • Available - on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: - 2
  • Available on UseGalaxy.fr: 2
  • Tools available - on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: - 2
  • Tools available on UseGalaxy.eu: 2
  • Tools - available on UseGalaxy.fr: 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 14941
  • No. of tool - users (all time) (usegalaxy.eu): 14941
  • Tool usage (5 years) - (usegalaxy.eu): 383
  • Tool usage (all time) (usegalaxy.eu): - 383
  • No. of tool users (5 years) (usegalaxy.org): 25941
  • No. - of tool users (all time) (usegalaxy.org): 25941
  • Tool usage - (5 years) (usegalaxy.org): 255
  • Tool usage (all time) (usegalaxy.org): - 255
  • No. of tool users (5 years) (usegalaxy.org.au): 2856
  • No. - of tool users (all time) (usegalaxy.org.au): 2856
  • Tool - usage (5 years) (usegalaxy.org.au): 112
  • Tool usage (all - time) (usegalaxy.org.au): 112
  • No. of tool users (5 years) - - all main servers: 43738
  • No. of tool users (all time) - - all main servers: 43738
  • Tool usage (5 years) - all main - servers: 750
  • Tool usage (all time) - all main servers: - 750
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: .nan title_md: suite_qiime2_core__tools - - description_md: '
  • Galaxy tool ids: Draw_phylogram
  • Description: - Draw phylogeny
  • bio.tool id: t2ps
  • bio.tool - ids: t2ps
  • biii: nan
  • bio.tool name: - Draw phylogeny
  • 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
  • EDAM operation: Phylogenetic tree visualisation
  • EDAM - topic: Phylogenomics
  • Status: To update
  • Source: - https://bitbucket.org/natefoo/taxonomy
  • ToolShed categories: - Metagenomics
  • ToolShed id: t2ps
  • Date of first - commit of the suite: 2014-01-27
  • Galaxy wrapper owner: - devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps
  • Galaxy - wrapper version: 1.0.0
  • Conda id: taxonomy
  • Conda - version: 0.10.0
  • EDAM operation (no superclasses): - Phylogenetic tree visualisation
  • EDAM topic (no superclasses): - Phylogenomics
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 411
  • No. of tool - users (all time) (usegalaxy.eu): 472
  • Tool usage (5 years) - (usegalaxy.eu): 68
  • Tool usage (all time) (usegalaxy.eu): - 90
  • No. of tool users (5 years) (usegalaxy.org): 102
  • No. - of tool users (all time) (usegalaxy.org): 7952
  • Tool usage - (5 years) (usegalaxy.org): 13
  • Tool usage (all time) (usegalaxy.org): - 1240
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 513
  • No. - of tool users (all time) - all main servers: 8424
  • Tool - usage (5 years) - all main servers: 81
  • Tool usage (all - time) - all main servers: 1330
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Draw phylogeny title_md: t2ps - - description_md: '
  • Galaxy tool ids: t2t_report
  • Description: - Summarize taxonomy
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: To update
  • Source: - https://bitbucket.org/natefoo/taxonomy
  • ToolShed categories: - Metagenomics
  • ToolShed id: t2t_report
  • Date - of first commit of the suite: 2014-01-27
  • Galaxy wrapper - owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report
  • Galaxy - wrapper version: 1.0.0
  • Conda id: taxonomy
  • Conda - version: 0.10.0
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 927
  • No. of tool - users (all time) (usegalaxy.eu): 959
  • Tool usage (5 years) - (usegalaxy.eu): 65
  • Tool usage (all time) (usegalaxy.eu): - 78
  • No. of tool users (5 years) (usegalaxy.org): 130
  • No. - of tool users (all time) (usegalaxy.org): 7194
  • Tool usage - (5 years) (usegalaxy.org): 18
  • Tool usage (all time) (usegalaxy.org): - 1143
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 1057
  • No. - of tool users (all time) - all main servers: 8153
  • Tool - usage (5 years) - all main servers: 83
  • Tool usage (all - time) - all main servers: 1221
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Summarize taxonomy title_md: t2t_report - - description_md: '
  • Galaxy tool ids: t_coffee
  • Description: - T-Coffee
  • bio.tool id: nan
  • bio.tool ids: - nan
  • biii: nan
  • bio.tool name: nan
  • bio.tool - description: nan
  • EDAM operation: nan
  • EDAM - topic: nan
  • Status: To update
  • Source: - http://www.tcoffee.org/
  • ToolShed categories: Sequence Analysis
  • ToolShed - id: t_coffee
  • Date of first commit of the suite: - 2016-12-13
  • Galaxy wrapper owner: earlhaminst
  • Galaxy - wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee
  • Galaxy - wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee
  • Galaxy - wrapper version: 13.45.0.4846264
  • Conda id: t-coffee
  • Conda - version: 13.46.0.919e8c6b
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 3783
  • No. of tool - users (all time) (usegalaxy.eu): 9125
  • Tool usage (5 years) - (usegalaxy.eu): 211
  • Tool usage (all time) (usegalaxy.eu): - 229
  • No. of tool users (5 years) (usegalaxy.org): 1
  • No. - of tool users (all time) (usegalaxy.org): 1
  • Tool usage - (5 years) (usegalaxy.org): 1
  • Tool usage (all time) (usegalaxy.org): - 1
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 3784
  • No. - of tool users (all time) - all main servers: 9126
  • Tool - usage (5 years) - all main servers: 212
  • Tool usage (all - time) - all main servers: 230
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: T-Coffee title_md: t_coffee - - description_md: '
  • Galaxy tool ids: taxonomy_krona_chart
  • Description: - Krona pie chart from taxonomic profile
  • bio.tool id: krona
  • bio.tool - ids: krona
  • biii: nan
  • bio.tool name: - Krona
  • bio.tool description: Krona creates interactive HTML5 - charts of hierarchical data (such as taxonomic abundance in a metagenome).
  • EDAM - operation: Visualisation
  • EDAM topic: Metagenomics
  • Status: - To update
  • Source: http://sourceforge.net/projects/krona/
  • ToolShed - categories: Assembly
  • ToolShed id: taxonomy_krona_chart
  • Date - of first commit of the suite: 2015-08-12
  • Galaxy wrapper - owner: crs4
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart
  • Galaxy - wrapper version: 2.7.1+galaxy0
  • Conda id: krona
  • Conda - version: 2.8.1
  • EDAM operation (no superclasses): - Visualisation
  • EDAM topic (no superclasses): Metagenomics
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 36069
  • No. of tool - users (all time) (usegalaxy.eu): 36922
  • Tool usage (5 years) - (usegalaxy.eu): 5257
  • Tool usage (all time) (usegalaxy.eu): - 5431
  • No. of tool users (5 years) (usegalaxy.org): 25255
  • No. - of tool users (all time) (usegalaxy.org): 30822
  • Tool usage - (5 years) (usegalaxy.org): 5066
  • Tool usage (all time) (usegalaxy.org): - 5826
  • No. of tool users (5 years) (usegalaxy.org.au): 7949
  • No. - of tool users (all time) (usegalaxy.org.au): 7949
  • Tool - usage (5 years) (usegalaxy.org.au): 1584
  • Tool usage (all - time) (usegalaxy.org.au): 1584
  • No. of tool users (5 years) - - all main servers: 69273
  • No. of tool users (all time) - - all main servers: 75693
  • Tool usage (5 years) - all main - servers: 11907
  • Tool usage (all time) - all main servers: - 12841
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Krona pie chart from taxonomic profile title_md: taxonomy_krona_chart - - description_md: '
  • Galaxy tool ids: tb_profiler_profile
  • Description: - Processes M. tuberculosis sequence data to infer strain type and identify known - drug resistance markers.
  • bio.tool id: tb-profiler
  • bio.tool - ids: tb-profiler
  • biii: nan
  • bio.tool - name: tb-profiler
  • bio.tool description: A tool for - drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, - alignments or variants).
  • EDAM operation: Antimicrobial - resistance prediction
  • EDAM topic: nan
  • Status: - To update
  • Source: https://github.com/jodyphelan/TBProfiler
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: tbprofiler
  • Date - of first commit of the suite: 2019-08-16
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler
  • Galaxy - wrapper version: 6.2.1
  • Conda id: tb-profiler
  • Conda - version: 6.3.0
  • EDAM operation (no superclasses): - Antimicrobial resistance prediction
  • EDAM topic (no superclasses): - nan
  • Available on UseGalaxy.org (Main): 1
  • Available - on UseGalaxy.org.au: 1
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 1
  • Tools available on UseGalaxy.org.au: - 1
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 1
  • Tools - available on UseGalaxy.cz: 1
  • Tools available on UseGalaxy.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 6372
  • No. of tool - users (all time) (usegalaxy.eu): 6395
  • Tool usage (5 years) - (usegalaxy.eu): 372
  • Tool usage (all time) (usegalaxy.eu): - 379
  • No. of tool users (5 years) (usegalaxy.org): 7339
  • No. - of tool users (all time) (usegalaxy.org): 7339
  • Tool usage - (5 years) (usegalaxy.org): 378
  • Tool usage (all time) (usegalaxy.org): - 378
  • No. of tool users (5 years) (usegalaxy.org.au): 6966
  • No. - of tool users (all time) (usegalaxy.org.au): 6966
  • Tool - usage (5 years) (usegalaxy.org.au): 154
  • Tool usage (all - time) (usegalaxy.org.au): 154
  • No. of tool users (5 years) - - all main servers: 20677
  • No. of tool users (all time) - - all main servers: 20700
  • Tool usage (5 years) - all main - servers: 904
  • Tool usage (all time) - all main servers: - 911
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Processes M. tuberculosis sequence data to infer strain type and + identify known drug resistance markers. title_md: tb-profiler - - description_md: '
  • Galaxy tool ids: tooldistillator, tooldistillator_summarize
  • Description: - ToolDistillator extract and aggregate information from different tool outputs - to JSON parsable files
  • bio.tool id: tooldistillator
  • bio.tool - ids: tooldistillator
  • biii: nan
  • bio.tool - name: ToolDistillator
  • 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.
  • EDAM - operation: Data handling, Parsing
  • EDAM topic: Microbiology, - Bioinformatics, Sequence analysis
  • Status: Up-to-date
  • Source: - https://gitlab.com/ifb-elixirfr/abromics/tooldistillator
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: tooldistillator
  • Date - of first commit of the suite: 2024-04-30
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator
  • Galaxy - wrapper version: 0.9.1
  • Conda id: tooldistillator
  • Conda - version: 0.9.1
  • EDAM operation (no superclasses): - Parsing
  • EDAM topic (no superclasses): Microbiology, Bioinformatics, - Sequence analysis
  • Available on UseGalaxy.org (Main): 2
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 2
  • Available on UseGalaxy.fr: 2
  • Tools available - on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 2
  • Tools - available on UseGalaxy.fr: 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: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 65
  • No. of tool - users (all time) (usegalaxy.eu): 65
  • Tool usage (5 years) - (usegalaxy.eu): 9
  • Tool usage (all time) (usegalaxy.eu): - 9
  • No. of tool users (5 years) (usegalaxy.org): 6
  • No. - of tool users (all time) (usegalaxy.org): 6
  • Tool usage - (5 years) (usegalaxy.org): 5
  • Tool usage (all time) (usegalaxy.org): - 5
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 71
  • No. - of tool users (all time) - all main servers: 71
  • Tool usage - (5 years) - all main servers: 14
  • Tool usage (all time) - - all main servers: 14
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: ToolDistillator extract and aggregate information from different + tool outputs to JSON parsable files title_md: tooldistillator - - description_md: '
  • Galaxy tool ids: gff_to_prot, transit_gumbel, - transit_hmm, transit_resampling, transit_tn5gaps
  • Description: - TRANSIT
  • bio.tool id: transit
  • bio.tool ids: - transit
  • biii: nan
  • bio.tool name: TRANSIT
  • 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.
  • EDAM operation: Transposon prediction
  • EDAM - topic: DNA, Sequencing, Mobile genetic elements
  • Status: - To update
  • Source: https://github.com/mad-lab/transit/
  • ToolShed - categories: Genome annotation
  • ToolShed id: nan
  • Date - of first commit of the suite: 2019-03-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit
  • Galaxy - wrapper version: 3.0.2
  • Conda id: transit
  • Conda - version: 3.2.3
  • EDAM operation (no superclasses): - Transposon prediction
  • EDAM topic (no superclasses): DNA, - Sequencing, Mobile genetic elements
  • Available on UseGalaxy.org - (Main): 5
  • Available on UseGalaxy.org.au: 5
  • Available - on UseGalaxy.eu: 5
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 5
  • Tools available on - UseGalaxy.org.au: 5
  • Tools available on UseGalaxy.eu: - 5
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools 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.no: 5
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1039
  • No. of tool users (all time) (usegalaxy.eu): 1039
  • Tool - usage (5 years) (usegalaxy.eu): 189
  • Tool usage (all time) - (usegalaxy.eu): 189
  • No. of tool users (5 years) (usegalaxy.org): - 2672
  • No. of tool users (all time) (usegalaxy.org): 3349
  • Tool - usage (5 years) (usegalaxy.org): 467
  • Tool usage (all time) - (usegalaxy.org): 485
  • No. of tool users (5 years) (usegalaxy.org.au): - 358
  • No. of tool users (all time) (usegalaxy.org.au): 358
  • Tool - usage (5 years) (usegalaxy.org.au): 47
  • Tool usage (all - time) (usegalaxy.org.au): 47
  • No. of tool users (5 years) - - all main servers: 4069
  • No. of tool users (all time) - - all main servers: 4746
  • Tool usage (5 years) - all main - servers: 703
  • Tool usage (all time) - all main servers: - 721
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: TRANSIT title_md: transit - - description_md: '
  • Galaxy tool ids: transtermhp
  • Description: - Finds rho-independent transcription terminators in bacterial genomes
  • bio.tool - id: transtermhp
  • bio.tool ids: transtermhp
  • biii: - nan
  • bio.tool name: TransTermHP
  • 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
  • EDAM operation: - Transcriptional regulatory element prediction
  • EDAM topic: - Transcription factors and regulatory sites
  • Status: To update
  • Source: - https://transterm.cbcb.umd.edu
  • ToolShed categories: Sequence - Analysis
  • ToolShed id: transtermhp
  • Date of - first commit of the suite: 2015-10-08
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp
  • Galaxy - wrapper version: nan
  • Conda id: transtermhp
  • Conda - version: 2.09
  • EDAM operation (no superclasses): - Transcriptional regulatory element prediction
  • EDAM topic (no superclasses): - Transcription factors and regulatory sites
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 1
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 250
  • No. of tool users (all time) (usegalaxy.eu): 254
  • Tool - usage (5 years) (usegalaxy.eu): 31
  • Tool usage (all time) - (usegalaxy.eu): 31
  • No. of tool users (5 years) (usegalaxy.org): - 174
  • No. of tool users (all time) (usegalaxy.org): 174
  • Tool - usage (5 years) (usegalaxy.org): 45
  • Tool usage (all time) - (usegalaxy.org): 45
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 424
  • No. of tool users (all time) - all main - servers: 428
  • Tool usage (5 years) - all main servers: - 76
  • Tool usage (all time) - all main servers: 76
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: Finds rho-independent transcription terminators in bacterial genomes title_md: transtermhp - - description_md: '
  • Galaxy tool ids: trim_galore
  • Description: - Trim Galore adaptive quality and adapter trimmer
  • bio.tool id: - trim_galore
  • bio.tool ids: trim_galore
  • biii: - nan
  • bio.tool name: Trim Galore
  • 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.
  • EDAM - operation: Sequence trimming, Primer removal, Read pre-processing
  • EDAM - topic: Sequence analysis
  • Status: To update
  • Source: - http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
  • ToolShed - categories: Sequence Analysis, Fastq Manipulation
  • ToolShed - id: trim_galore
  • Date of first commit of the suite: - 2015-04-22
  • Galaxy wrapper owner: bgruening
  • Galaxy - wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore
  • Galaxy - wrapper version: 0.6.7
  • Conda id: trim-galore
  • Conda - version: 0.6.10
  • EDAM operation (no superclasses): - Sequence trimming, Primer removal, Read pre-processing
  • EDAM topic - (no superclasses): Sequence analysis
  • Available on UseGalaxy.org - (Main): 1
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 229489
  • No. of tool users (all time) (usegalaxy.eu): 275008
  • Tool - usage (5 years) (usegalaxy.eu): 5733
  • Tool usage (all time) - (usegalaxy.eu): 6500
  • No. of tool users (5 years) (usegalaxy.org): - 228708
  • No. of tool users (all time) (usegalaxy.org): 324716
  • Tool - usage (5 years) (usegalaxy.org): 11708
  • Tool usage (all - time) (usegalaxy.org): 16638
  • No. of tool users (5 years) - (usegalaxy.org.au): 22644
  • No. of tool users (all time) - (usegalaxy.org.au): 23869
  • Tool usage (5 years) (usegalaxy.org.au): - 1439
  • Tool usage (all time) (usegalaxy.org.au): 1527
  • No. - of tool users (5 years) - all main servers: 480841
  • No. - of tool users (all time) - all main servers: 623593
  • Tool - usage (5 years) - all main servers: 18880
  • Tool usage (all - time) - all main servers: 24665
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Trim Galore adaptive quality and adapter trimmer title_md: trim_galore - - description_md: '
  • Galaxy tool ids: trycycler_cluster, trycycler_consensus, - trycycler_partition, trycycler_reconcile_msa, trycycler_subsample
  • Description: - Trycycler toolkit wrappers
  • bio.tool id: nan
  • bio.tool - ids: nan
  • biii: nan
  • bio.tool name: - nan
  • bio.tool description: nan
  • EDAM operation: - nan
  • EDAM topic: nan
  • Status: Up-to-date
  • Source: - https://github.com/rrwick/Trycycler
  • ToolShed categories: - Assembly
  • ToolShed id: trycycler
  • Date of first - commit of the suite: 2021-02-11
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler
  • Galaxy - wrapper version: 0.5.5
  • Conda id: trycycler
  • Conda - version: 0.5.5
  • EDAM operation (no superclasses): - nan
  • EDAM topic (no superclasses): nan
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 5
  • Available on UseGalaxy.eu: 5
  • Available - on UseGalaxy.fr: 5
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 5
  • Tools - available on UseGalaxy.eu: 5
  • Tools available on UseGalaxy.fr: - 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: - 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 14681
  • No. of tool - users (all time) (usegalaxy.eu): 14681
  • Tool usage (5 years) - (usegalaxy.eu): 265
  • Tool usage (all time) (usegalaxy.eu): - 265
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 4488
  • No. - of tool users (all time) (usegalaxy.org.au): 4488
  • Tool - usage (5 years) (usegalaxy.org.au): 147
  • Tool usage (all - time) (usegalaxy.org.au): 147
  • No. of tool users (5 years) - - all main servers: 19169
  • No. of tool users (all time) - - all main servers: 19169
  • Tool usage (5 years) - all main - servers: 412
  • Tool usage (all time) - all main servers: - 412
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Trycycler toolkit wrappers title_md: trycycler - - description_md: '
  • Galaxy tool ids: unicycler
  • Description: - Unicycler is a hybrid assembly pipeline for bacterial genomes.
  • bio.tool - id: unicycler
  • bio.tool ids: unicycler
  • biii: - nan
  • bio.tool name: Unicycler
  • bio.tool description: - A tool for assembling bacterial genomes from a combination of short (2nd generation) - and long (3rd generation) sequencing reads.
  • EDAM operation: - Genome assembly, Aggregation
  • EDAM topic: Microbiology, - Genomics, Sequencing, Sequence assembly
  • Status: Up-to-date
  • Source: - https://github.com/rrwick/Unicycler
  • ToolShed categories: - Assembly
  • ToolShed id: unicycler
  • Date of first - commit of the suite: 2018-08-28
  • Galaxy wrapper owner: - iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler
  • Galaxy - wrapper version: 0.5.1
  • Conda id: unicycler
  • Conda - version: 0.5.1
  • EDAM operation (no superclasses): - Genome assembly, Aggregation
  • EDAM topic (no superclasses): - Microbiology, Genomics, Sequencing, Sequence assembly
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 1
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 1
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 74120
  • No. of tool - users (all time) (usegalaxy.eu): 77648
  • Tool usage (5 years) - (usegalaxy.eu): 3798
  • Tool usage (all time) (usegalaxy.eu): - 3963
  • No. of tool users (5 years) (usegalaxy.org): 64946
  • No. - of tool users (all time) (usegalaxy.org): 90075
  • Tool usage - (5 years) (usegalaxy.org): 5451
  • Tool usage (all time) (usegalaxy.org): - 7380
  • No. of tool users (5 years) (usegalaxy.org.au): 19516
  • No. - of tool users (all time) (usegalaxy.org.au): 20422
  • Tool - usage (5 years) (usegalaxy.org.au): 2010
  • Tool usage (all - time) (usegalaxy.org.au): 2080
  • No. of tool users (5 years) - - all main servers: 158582
  • No. of tool users (all time) - - all main servers: 188145
  • Tool usage (5 years) - all main - servers: 11259
  • Tool usage (all time) - all main servers: - 13423
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Unicycler is a hybrid assembly pipeline for bacterial genomes. title_md: unicycler - - description_md: '
  • Galaxy tool ids: unipept
  • Description: - Unipept retrieves metaproteomics information
  • bio.tool id: - unipept
  • bio.tool ids: unipept
  • biii: - nan
  • bio.tool name: Unipept
  • bio.tool description: - Metaproteomics data analysis with a focus on interactive data visualizations.
  • EDAM - operation: Prediction and recognition, Visualisation
  • EDAM - topic: Proteomics, Proteogenomics, Biodiversity, Workflows
  • Status: - To update
  • Source: https://github.com/galaxyproteomics/tools-galaxyp
  • ToolShed - categories: Proteomics
  • ToolShed id: unipept
  • Date - of first commit of the suite: 2015-04-03
  • Galaxy wrapper - owner: galaxyp
  • Galaxy wrapper source: https://unipept.ugent.be/apidocs
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept
  • Galaxy - wrapper version: 4.5.1
  • Conda id: python
  • Conda - version: nan
  • EDAM operation (no superclasses): Prediction - and recognition, Visualisation
  • EDAM topic (no superclasses): - Proteomics, Proteogenomics, Biodiversity, Workflows
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 4900
  • No. of tool - users (all time) (usegalaxy.eu): 5146
  • Tool usage (5 years) - (usegalaxy.eu): 257
  • Tool usage (all time) (usegalaxy.eu): - 270
  • No. of tool users (5 years) (usegalaxy.org): 251
  • No. - of tool users (all time) (usegalaxy.org): 251
  • Tool usage - (5 years) (usegalaxy.org): 81
  • Tool usage (all time) (usegalaxy.org): - 81
  • No. of tool users (5 years) (usegalaxy.org.au): 1069
  • No. - of tool users (all time) (usegalaxy.org.au): 1069
  • Tool - usage (5 years) (usegalaxy.org.au): 29
  • Tool usage (all - time) (usegalaxy.org.au): 29
  • No. of tool users (5 years) - - all main servers: 6220
  • No. of tool users (all time) - - all main servers: 6466
  • Tool usage (5 years) - all main - servers: 367
  • Tool usage (all time) - all main servers: - 380
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Unipept retrieves metaproteomics information title_md: unipept - - description_md: '
  • Galaxy tool ids: uniprotxml_downloader
  • Description: - Download UniProt proteome in XML or fasta format
  • bio.tool id: - nan
  • bio.tool ids: nan
  • biii: nan
  • bio.tool - name: nan
  • bio.tool description: nan
  • EDAM - operation: nan
  • EDAM topic: nan
  • Status: - To update
  • Source: nan
  • ToolShed categories: - Proteomics
  • ToolShed id: uniprotxml_downloader
  • Date - of first commit of the suite: 2016-03-08
  • Galaxy wrapper - owner: galaxyp
  • Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader
  • Galaxy - wrapper version: 2.4.0
  • Conda id: requests
  • Conda - version: nan
  • EDAM operation (no superclasses): nan
  • EDAM - topic (no superclasses): nan
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 1
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 1
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - on Palfinder: 0
  • Tools available on PepSimili: 0
  • Tools - available on PhagePromotor: 0
  • Tools available on UseGalaxy.be: - 0
  • Tools available on UseGalaxy.cz: 1
  • Tools - available on UseGalaxy.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1488
  • No. of tool users (all time) (usegalaxy.eu): 1596
  • Tool - usage (5 years) (usegalaxy.eu): 230
  • Tool usage (all time) - (usegalaxy.eu): 266
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 743
  • No. of tool users (all time) (usegalaxy.org.au): 743
  • Tool - usage (5 years) (usegalaxy.org.au): 35
  • Tool usage (all - time) (usegalaxy.org.au): 35
  • No. of tool users (5 years) - - all main servers: 2231
  • No. of tool users (all time) - - all main servers: 2339
  • Tool usage (5 years) - all main - servers: 265
  • Tool usage (all time) - all main servers: - 301
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Download UniProt proteome in XML or fasta format title_md: uniprotxml_downloader - - description_md: '
  • Galaxy tool ids: usher_matutils, usher
  • Description: - UShER toolkit wrappers
  • bio.tool id: usher
  • bio.tool - ids: usher
  • biii: nan
  • bio.tool name: - usher
  • 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.
  • EDAM - operation: Classification, Phylogenetic tree visualisation, Phylogenetic - inference (from molecular sequences)
  • EDAM topic: Phylogeny, - Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics
  • Status: - To update
  • Source: https://github.com/yatisht/usher
  • ToolShed - categories: Phylogenetics
  • ToolShed id: usher
  • Date - of first commit of the suite: 2021-05-11
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher
  • Galaxy - wrapper version: 0.2.1
  • Conda id: usher
  • Conda - version: 0.6.3
  • EDAM operation (no superclasses): - Classification, Phylogenetic tree visualisation, Phylogenetic inference (from - molecular sequences)
  • EDAM topic (no superclasses): Cladistics, - Genotype and phenotype, Phylogenomics
  • Available on UseGalaxy.org - (Main): 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 2
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 2
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available on Dintor: - 0
  • Tools available on GASLINI: 0
  • Tools available - on Galaxy@AuBi: 0
  • Tools available on Galaxy@Pasteur: - 0
  • Tools available on GalaxyTrakr: 0
  • Tools - available on Genomic Hyperbrowser: 0
  • Tools available on - GigaGalaxy: 0
  • Tools available on HyPhy HIV NGS Tools: - 0
  • Tools available on IPK Galaxy Blast Suite: 0
  • Tools - available on ImmPort Galaxy: 0
  • Tools available on InteractoMIX: - 0
  • Tools available on MISSISSIPPI: 0
  • Tools - available on Mandoiu Lab: 0
  • Tools available on MiModD NacreousMap: - 0
  • Tools available on Oqtans: 0
  • Tools available - 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.no: 0
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1060
  • No. of tool users (all time) (usegalaxy.eu): 1060
  • Tool - usage (5 years) (usegalaxy.eu): 5
  • Tool usage (all time) - (usegalaxy.eu): 5
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 1060
  • No. of tool users (all time) - all main - servers: 1060
  • Tool usage (5 years) - all main servers: - 5
  • Tool usage (all time) - all main servers: 5
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: UShER toolkit wrappers title_md: usher - - description_md: '
  • Galaxy tool ids: valet
  • Description: - A pipeline for detecting mis-assemblies in metagenomic assemblies.
  • bio.tool - id: valet
  • bio.tool ids: valet
  • biii: - nan
  • bio.tool name: VALET
  • bio.tool description: - VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.
  • EDAM - operation: Sequence assembly, Sequence assembly visualisation
  • EDAM - topic: Metagenomics, Sequence assembly
  • Status: To - update
  • Source: https://github.com/marbl/VALET
  • ToolShed - categories: Metagenomics
  • ToolShed id: valet
  • Date - of first commit of the suite: 2017-11-16
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet
  • Galaxy - wrapper version: nan
  • Conda id: valet
  • Conda - version: 1.0
  • EDAM operation (no superclasses): Sequence - assembly, Sequence assembly visualisation
  • EDAM topic (no superclasses): - Metagenomics, Sequence assembly
  • Available on UseGalaxy.org (Main): - 1
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 1
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 518
  • No. of tool users (all time) (usegalaxy.eu): 677
  • Tool - usage (5 years) (usegalaxy.eu): 75
  • Tool usage (all time) - (usegalaxy.eu): 87
  • No. of tool users (5 years) (usegalaxy.org): - 234
  • No. of tool users (all time) (usegalaxy.org): 234
  • Tool - usage (5 years) (usegalaxy.org): 65
  • Tool usage (all time) - (usegalaxy.org): 65
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 752
  • No. of tool users (all time) - all main - servers: 911
  • Tool usage (5 years) - all main servers: - 140
  • Tool usage (all time) - all main servers: 152
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: A pipeline for detecting mis-assemblies in metagenomic assemblies. title_md: valet - - description_md: '
  • Galaxy tool ids: vapor
  • Description: - Classify Influenza samples from raw short read sequence data
  • bio.tool - id: vapor
  • bio.tool ids: vapor
  • biii: - nan
  • bio.tool name: VAPOR
  • 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.
  • EDAM operation: Data retrieval, De-novo assembly, - Read mapping
  • EDAM topic: Whole genome sequencing, Mapping, - Sequence assembly
  • Status: Up-to-date
  • Source: - https://github.com/connor-lab/vapor
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: vapor
  • Date - of first commit of the suite: 2022-08-24
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor
  • Galaxy - wrapper version: 1.0.2
  • Conda id: vapor
  • Conda - version: 1.0.2
  • EDAM operation (no superclasses): - Data retrieval, De-novo assembly, Read mapping
  • EDAM topic (no - superclasses): Whole genome sequencing, Mapping, Sequence assembly
  • Available - on UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 5936
  • No. of tool - users (all time) (usegalaxy.eu): 5936
  • Tool usage (5 years) - (usegalaxy.eu): 147
  • Tool usage (all time) (usegalaxy.eu): - 147
  • No. of tool users (5 years) (usegalaxy.org): 523
  • No. - of tool users (all time) (usegalaxy.org): 523
  • Tool usage - (5 years) (usegalaxy.org): 15
  • Tool usage (all time) (usegalaxy.org): - 15
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 6459
  • No. - of tool users (all time) - all main servers: 6459
  • Tool - usage (5 years) - all main servers: 162
  • Tool usage (all - time) - all main servers: 162
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Classify Influenza samples from raw short read sequence data title_md: vapor - - description_md: '
  • Galaxy tool ids: varvamp
  • Description: - Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse - viruses
  • bio.tool id: varvamp
  • bio.tool ids: - varvamp
  • biii: nan
  • bio.tool name: varVAMP
  • 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.
  • EDAM operation: PCR primer design
  • EDAM - topic: Virology, Probes and primers
  • Status: To update
  • Source: - https://github.com/jonas-fuchs/varVAMP/
  • ToolShed categories: - Sequence Analysis
  • ToolShed id: varvamp
  • Date - of first commit of the suite: 2024-01-27
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/jonas-fuchs/varVAMP
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp
  • Galaxy - wrapper version: 1.2.0
  • Conda id: varvamp
  • Conda - version: 1.2.1
  • EDAM operation (no superclasses): - PCR primer design
  • EDAM topic (no superclasses): Virology, - Probes and primers
  • Available on UseGalaxy.org (Main): 0
  • Available - on UseGalaxy.org.au: 0
  • Available on UseGalaxy.eu: - 1
  • Available on UseGalaxy.fr: 0
  • Tools available - on UseGalaxy.org (Main): 0
  • Tools available on UseGalaxy.org.au: - 0
  • Tools available on UseGalaxy.eu: 1
  • Tools - available on UseGalaxy.fr: 0
  • Tools available on APOSTL: - 0
  • Tools available on ARGs-OAP: 0
  • Tools available - on CIRM-CFBP: 0
  • Tools available on ChemFlow: 0
  • Tools - available on Coloc-stats: 0
  • Tools available on CropGalaxy: - 0
  • Tools available on Dintor: 0
  • Tools available - on GASLINI: 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 273
  • No. of tool - users (all time) (usegalaxy.eu): 273
  • Tool usage (5 years) - (usegalaxy.eu): 12
  • Tool usage (all time) (usegalaxy.eu): - 12
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 273
  • No. - of tool users (all time) - all main servers: 273
  • Tool usage - (5 years) - all main servers: 12
  • Tool usage (all time) - - all main servers: 12
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: Variable VirusAMPlicons (varVAMP) is a tool to design primers + for highly diverse viruses title_md: varvamp - - description_md: '
  • Galaxy tool ids: vegan_diversity, vegan_fisher_alpha, - vegan_rarefaction
  • Description: an R package fo community - ecologist
  • bio.tool id: vegan
  • bio.tool ids: - vegan
  • biii: nan
  • bio.tool name: vegan
  • bio.tool - description: Ordination methods, diversity analysis and other functions - for community and vegetation ecologists
  • EDAM operation: - Standardisation and normalisation, Analysis
  • EDAM topic: - Ecology, Phylogenetics, Environmental science
  • Status: To - update
  • Source: https://cran.r-project.org/package=vegan
  • ToolShed - categories: Metagenomics
  • ToolShed id: nan
  • Date - of first commit of the suite: 2015-08-27
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan
  • Galaxy - wrapper version: 2.4-3
  • Conda id: r-vegan
  • Conda - version: 2.3_4
  • EDAM operation (no superclasses): - Standardisation and normalisation, Analysis
  • EDAM topic (no superclasses): - Ecology, Phylogenetics, Environmental science
  • Available on UseGalaxy.org - (Main): 3
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 3
  • Available on UseGalaxy.fr: 0
  • Tools - available on UseGalaxy.org (Main): 3
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 3
  • Tools available on UseGalaxy.fr: 0
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 3
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 2157
  • No. of tool users (all time) (usegalaxy.eu): 2287
  • Tool - usage (5 years) (usegalaxy.eu): 198
  • Tool usage (all time) - (usegalaxy.eu): 209
  • No. of tool users (5 years) (usegalaxy.org): - 3930
  • No. of tool users (all time) (usegalaxy.org): 5591
  • Tool - usage (5 years) (usegalaxy.org): 446
  • Tool usage (all time) - (usegalaxy.org): 744
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 6087
  • No. of tool users (all time) - all main - servers: 7878
  • Tool usage (5 years) - all main servers: - 644
  • Tool usage (all time) - all main servers: 953
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: an R package fo community ecologist title_md: vegan - - description_md: '
  • Galaxy tool ids: velvetg, velveth
  • Description: - de novo genomic assembler specially designed for short read sequencing technologies
  • bio.tool - id: velvet
  • bio.tool ids: velvet
  • biii: - nan
  • bio.tool name: Velvet
  • bio.tool description: - A de novo genomic assembler specially designed for short read sequencing technologies, - such as Solexa or 454 or SOLiD.
  • EDAM operation: Formatting, - De-novo assembly
  • EDAM topic: Sequence assembly
  • Status: - To update
  • Source: https://www.ebi.ac.uk/~zerbino/velvet/
  • ToolShed - categories: Assembly
  • ToolShed id: velvet
  • Date - of first commit of the suite: 2020-06-09
  • Galaxy wrapper - owner: devteam
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet
  • Galaxy - wrapper version: nan
  • Conda id: velvet
  • Conda - version: 1.2.10
  • EDAM operation (no superclasses): - Formatting, De-novo assembly
  • EDAM topic (no superclasses): - Sequence assembly
  • Available on UseGalaxy.org (Main): 2
  • Available - on UseGalaxy.org.au: 2
  • Available on UseGalaxy.eu: - 2
  • Available on UseGalaxy.fr: 2
  • Tools available - on UseGalaxy.org (Main): 2
  • Tools available on UseGalaxy.org.au: - 2
  • Tools available on UseGalaxy.eu: 2
  • Tools - available on UseGalaxy.fr: 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: 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.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 25171
  • No. of tool - users (all time) (usegalaxy.eu): 27943
  • Tool usage (5 years) - (usegalaxy.eu): 3899
  • Tool usage (all time) (usegalaxy.eu): - 4270
  • No. of tool users (5 years) (usegalaxy.org): 51187
  • No. - of tool users (all time) (usegalaxy.org): 51187
  • Tool usage - (5 years) (usegalaxy.org): 7557
  • Tool usage (all time) (usegalaxy.org): - 7557
  • No. of tool users (5 years) (usegalaxy.org.au): 28546
  • No. - of tool users (all time) (usegalaxy.org.au): 28619
  • Tool - usage (5 years) (usegalaxy.org.au): 3585
  • Tool usage (all - time) (usegalaxy.org.au): 3613
  • No. of tool users (5 years) - - all main servers: 104904
  • No. of tool users (all time) - - all main servers: 107749
  • Tool usage (5 years) - all main - servers: 15041
  • Tool usage (all time) - all main servers: - 15440
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: de novo genomic assembler specially designed for short read sequencing + technologies title_md: velvet - - description_md: '
  • Galaxy tool ids: velvetoptimiser
  • Description: - Automatically optimize Velvet assemblies
  • bio.tool id: velvetoptimiser
  • bio.tool - ids: velvetoptimiser
  • biii: nan
  • bio.tool - name: VelvetOptimiser
  • 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.
  • EDAM - operation: Optimisation and refinement, Sequence assembly
  • EDAM - topic: Genomics, Sequence assembly
  • Status: To update
  • Source: - nan
  • ToolShed categories: Assembly
  • ToolShed - id: velvetoptimiser
  • Date of first commit of the suite: - 2017-12-19
  • Galaxy wrapper owner: simon-gladman
  • Galaxy - wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser
  • Galaxy - wrapper version: 2.2.6+galaxy2
  • Conda id: velvet
  • Conda - version: 1.2.10
  • EDAM operation (no superclasses): - Optimisation and refinement, Sequence assembly
  • EDAM topic (no - superclasses): Genomics, Sequence assembly
  • Available on - UseGalaxy.org (Main): 1
  • Available on UseGalaxy.org.au: - 1
  • Available on UseGalaxy.eu: 1
  • Available - on UseGalaxy.fr: 0
  • Tools available on UseGalaxy.org (Main): - 1
  • Tools available on UseGalaxy.org.au: 1
  • Tools - available on UseGalaxy.eu: 1
  • Tools available on UseGalaxy.fr: - 0
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available 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.no: - 1
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 4715
  • No. of tool - users (all time) (usegalaxy.eu): 5343
  • Tool usage (5 years) - (usegalaxy.eu): 888
  • Tool usage (all time) (usegalaxy.eu): - 965
  • No. of tool users (5 years) (usegalaxy.org): 9575
  • No. - of tool users (all time) (usegalaxy.org): 9576
  • Tool usage - (5 years) (usegalaxy.org): 2117
  • Tool usage (all time) (usegalaxy.org): - 2117
  • No. of tool users (5 years) (usegalaxy.org.au): 3271
  • No. - of tool users (all time) (usegalaxy.org.au): 5524
  • Tool - usage (5 years) (usegalaxy.org.au): 1050
  • Tool usage (all - time) (usegalaxy.org.au): 1397
  • No. of tool users (5 years) - - all main servers: 17561
  • No. of tool users (all time) - - all main servers: 20443
  • Tool usage (5 years) - all main - servers: 4055
  • Tool usage (all time) - all main servers: - 4479
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: Automatically optimize Velvet assemblies title_md: velvet_optimiser - - description_md: '
  • Galaxy tool ids: virannot_blast2tsv, virannot_otu, - virAnnot_rps2tsv
  • Description: virAnnot wrappers
  • bio.tool - id: virannot
  • bio.tool ids: virannot
  • biii: - nan
  • bio.tool name: virAnnot
  • 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.
  • EDAM operation: Sequence - annotation, Sequence clustering, Sequence cluster visualisation
  • EDAM - topic: Metagenomics, Virology, Microbial ecology
  • Status: - To update
  • Source: https://github.com/marieBvr/virAnnot
  • ToolShed - categories: Metagenomics
  • ToolShed id: virannot
  • Date - of first commit of the suite: 2024-03-04
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot
  • Galaxy - wrapper version: 1.1.0+galaxy0
  • Conda id: biopython
  • Conda - version: 1.70
  • EDAM operation (no superclasses): - Sequence annotation, Sequence clustering, Sequence cluster visualisation
  • EDAM - topic (no superclasses): Metagenomics, Virology, Microbial ecology
  • Available - on UseGalaxy.org (Main): 0
  • Available on UseGalaxy.org.au: - 0
  • Available on UseGalaxy.eu: 3
  • Available - on UseGalaxy.fr: 3
  • Tools available on UseGalaxy.org (Main): - 0
  • Tools available on UseGalaxy.org.au: 0
  • Tools - available on UseGalaxy.eu: 3
  • Tools available on UseGalaxy.fr: - 3
  • Tools available on APOSTL: 0
  • Tools available - on ARGs-OAP: 0
  • Tools available on CIRM-CFBP: 0
  • Tools - available on ChemFlow: 0
  • Tools available on Coloc-stats: - 0
  • Tools available on CropGalaxy: 0
  • Tools - available on Dintor: 0
  • Tools available on GASLINI: - 0
  • Tools available on Galaxy@AuBi: 0
  • Tools - available on Galaxy@Pasteur: 0
  • Tools available on GalaxyTrakr: - 0
  • Tools available on Genomic Hyperbrowser: 0
  • Tools - available on GigaGalaxy: 0
  • Tools available on HyPhy HIV - NGS Tools: 0
  • Tools available on IPK Galaxy Blast Suite: - 0
  • Tools available on ImmPort Galaxy: 0
  • Tools - available on InteractoMIX: 0
  • Tools available on MISSISSIPPI: - 0
  • Tools available on Mandoiu Lab: 0
  • Tools - available on MiModD NacreousMap: 0
  • Tools available on Oqtans: - 0
  • Tools available on Palfinder: 0
  • Tools available - on PepSimili: 0
  • Tools available on PhagePromotor: - 0
  • Tools available on UseGalaxy.be: 0
  • Tools - available on UseGalaxy.cz: 0
  • Tools available on UseGalaxy.no: - 0
  • Tools available on Viral Variant Visualizer (VVV): 0
  • No. - of tool users (5 years) (usegalaxy.eu): 94
  • No. of tool - users (all time) (usegalaxy.eu): 94
  • Tool usage (5 years) - (usegalaxy.eu): 16
  • Tool usage (all time) (usegalaxy.eu): - 16
  • No. of tool users (5 years) (usegalaxy.org): 0
  • No. - of tool users (all time) (usegalaxy.org): 0
  • Tool usage - (5 years) (usegalaxy.org): 0
  • Tool usage (all time) (usegalaxy.org): - 0
  • No. of tool users (5 years) (usegalaxy.org.au): 0
  • No. - of tool users (all time) (usegalaxy.org.au): 0
  • Tool usage - (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) (usegalaxy.org.au): - 0
  • No. of tool users (5 years) - all main servers: 94
  • No. - of tool users (all time) - all main servers: 94
  • Tool usage - (5 years) - all main servers: 16
  • Tool usage (all time) - - all main servers: 16
  • Reviewed: True
  • To - keep: True
  • Deprecated: False
' + - description_md: virAnnot wrappers title_md: virAnnot - - description_md: '
  • Galaxy tool ids: vsearch_alignment, vsearch_chimera_detection, - vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, - vsearch_shuffling, vsearch_sorting
  • Description: VSEARCH - including searching, clustering, chimera detection, dereplication, sorting, - masking and shuffling of sequences.
  • bio.tool id: vsearch
  • bio.tool - ids: vsearch
  • biii: nan
  • bio.tool name: - VSEARCH
  • 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.
  • EDAM operation: DNA mapping, Chimera detection
  • EDAM - topic: Metagenomics, Sequence analysis
  • Status: To - update
  • Source: https://github.com/torognes/vsearch
  • ToolShed - categories: Sequence Analysis
  • ToolShed id: vsearch
  • Date - of first commit of the suite: 2015-07-01
  • Galaxy wrapper - owner: iuc
  • Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch
  • Galaxy - wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch
  • Galaxy - wrapper version: 2.8.3
  • Conda id: vsearch
  • Conda - version: 2.29.0
  • EDAM operation (no superclasses): - DNA mapping, Chimera detection
  • EDAM topic (no superclasses): - Metagenomics, Sequence analysis
  • Available on UseGalaxy.org (Main): - 8
  • Available on UseGalaxy.org.au: 8
  • Available - on UseGalaxy.eu: 8
  • Available on UseGalaxy.fr: 8
  • Tools - available on UseGalaxy.org (Main): 8
  • Tools available on - UseGalaxy.org.au: 8
  • Tools available on UseGalaxy.eu: - 8
  • Tools available on UseGalaxy.fr: 8
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available 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.no: 8
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 9694
  • No. of tool users (all time) (usegalaxy.eu): 10338
  • Tool - usage (5 years) (usegalaxy.eu): 559
  • Tool usage (all time) - (usegalaxy.eu): 628
  • No. of tool users (5 years) (usegalaxy.org): - 12282
  • No. of tool users (all time) (usegalaxy.org): 53546
  • Tool - usage (5 years) (usegalaxy.org): 1031
  • Tool usage (all time) - (usegalaxy.org): 2007
  • No. of tool users (5 years) (usegalaxy.org.au): - 5334
  • No. of tool users (all time) (usegalaxy.org.au): 5672
  • Tool - usage (5 years) (usegalaxy.org.au): 246
  • Tool usage (all - time) (usegalaxy.org.au): 277
  • No. of tool users (5 years) - - all main servers: 27310
  • No. of tool users (all time) - - all main servers: 69556
  • Tool usage (5 years) - all main - servers: 1836
  • Tool usage (all time) - all main servers: - 2912
  • Reviewed: True
  • To keep: True
  • Deprecated: - False
' + - description_md: VSEARCH including searching, clustering, chimera detection, dereplication, + sorting, masking and shuffling of sequences. title_md: vsearch - - description_md: '
  • Galaxy tool ids: wtdbg
  • Description: - WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.
  • bio.tool - id: wtdbg2
  • bio.tool ids: wtdbg2
  • biii: - nan
  • bio.tool name: wtdbg2
  • 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.
  • EDAM operation: Genome assembly, De-novo - assembly
  • EDAM topic: Sequence assembly, Sequencing
  • Status: - Up-to-date
  • Source: https://github.com/ruanjue/wtdbg2
  • ToolShed - categories: Assembly
  • ToolShed id: wtdbg
  • Date - of first commit of the suite: 2018-06-12
  • Galaxy wrapper - owner: bgruening
  • Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg
  • Galaxy - wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg
  • Galaxy - wrapper version: 2.5
  • Conda id: wtdbg
  • Conda - version: 2.5
  • EDAM operation (no superclasses): Genome - assembly, De-novo assembly
  • EDAM topic (no superclasses): - Sequence assembly, Sequencing
  • Available on UseGalaxy.org (Main): - 0
  • Available on UseGalaxy.org.au: 0
  • Available - on UseGalaxy.eu: 1
  • Available on UseGalaxy.fr: 1
  • Tools - available on UseGalaxy.org (Main): 0
  • Tools available on - UseGalaxy.org.au: 0
  • Tools available on UseGalaxy.eu: - 1
  • Tools available on UseGalaxy.fr: 1
  • Tools - available on APOSTL: 0
  • Tools available on ARGs-OAP: - 0
  • Tools available on CIRM-CFBP: 0
  • Tools available - on ChemFlow: 0
  • Tools available on Coloc-stats: 0
  • Tools - available on CropGalaxy: 0
  • Tools available 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.no: 1
  • Tools available on Viral Variant - Visualizer (VVV): 0
  • No. of tool users (5 years) (usegalaxy.eu): - 1619
  • No. of tool users (all time) (usegalaxy.eu): 1715
  • Tool - usage (5 years) (usegalaxy.eu): 337
  • Tool usage (all time) - (usegalaxy.eu): 376
  • No. of tool users (5 years) (usegalaxy.org): - 0
  • No. of tool users (all time) (usegalaxy.org): 0
  • Tool - usage (5 years) (usegalaxy.org): 0
  • Tool usage (all time) - (usegalaxy.org): 0
  • No. of tool users (5 years) (usegalaxy.org.au): - 0
  • No. of tool users (all time) (usegalaxy.org.au): 0
  • Tool - usage (5 years) (usegalaxy.org.au): 0
  • Tool usage (all time) - (usegalaxy.org.au): 0
  • No. of tool users (5 years) - all - main servers: 1619
  • No. of tool users (all time) - all main - servers: 1715
  • Tool usage (5 years) - all main servers: - 337
  • Tool usage (all time) - all main servers: 376
  • Reviewed: - True
  • To keep: True
  • Deprecated: False
' + - description_md: WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads + assembly. title_md: wtdbg id: tool_list title: List of community curated tools available for microGalaxy From f72d09a55997da3db1887294d0c780329a12a27d Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 16:30:15 +0100 Subject: [PATCH 13/38] multiple tools --- .../microgalaxy/lab/sections/5_tools.yml | 752 +----------------- 1 file changed, 11 insertions(+), 741 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 77e11abf..11a75ac8 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -1,744 +1,14 @@ id: tools +title: Community Tools tabs: -- content: - - description_md: Tools to compute and analyse biodiversity metrics - title_md: PAMPA - - description_md: TreeBeST best - title_md: TreeBest - - description_md: Order and Orientate Contigs - title_md: abacas - - description_md: Mass screening of contigs for antiobiotic resistance genes - title_md: abricate - - description_md: A pipeline for running AMRfinderPlus and collating results into - functional classes - title_md: abritamr - - description_md: Assembly By Short Sequences - a de novo, parallel, paired-end - sequence assembler - title_md: abyss - - description_md: Performs analysis Of differential abundance taking sample variation - into account - title_md: aldex2 - - description_md: AmpliCan is an analysis tool for genome editing. - title_md: amplican - - description_md: '"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.' - title_md: amrfinderplus - - description_md: Performs analysis of compositions of microbiomes with bias correction. - title_md: ancombc - - description_md: Antismash allows the genome-wide identification, annotation and - analysis of secondary metabolite biosynthesis gene clusters - title_md: antismash - - description_md: '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' - title_md: artic - - description_md: Summarise an assembly (e.g. N50 metrics) - title_md: assemblystats - - description_md: '"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."' - title_md: bakta - - description_md: Operate on and transform BAM datasets in various ways using bamtools - title_md: bamtools - - description_md: Bandage - A Bioinformatics Application for Navigating De novo - Assembly Graphs Easily - title_md: bandage - - description_md: Detecting natural selection from population-based genetic data - title_md: bayescan - - description_md: 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. - title_md: bbtools - - description_md: Construct sequence similarity networks of BGCs and groups them - into GCF - title_md: bigscape - - description_md: Reconciles the outputs of different binning programs with the - aim to improve the quality of genome bins,especially with respect to contamination - levels. - title_md: binning_refiner - - description_md: Heidelberg and Enteritidis SNP Elucidation - title_md: biohansel - - description_md: The biom-format package provides a command line interface and - Python API for working with BIOM files. - title_md: biom_format - - description_md: Bio-Tradis is a tool suite dedicated to essentiality analyses - with TraDis data. - title_md: biotradis - - description_md: Maps BLAST results to GO annotation terms - title_md: blast2go - - description_md: BLAST Reciprocal Best Hits (RBH) from two FASTA files - title_md: blast_rbh - - description_md: Make table of top BLAST match descriptions - title_md: blastxml_to_top_descr - - description_md: Bayesian Reestimation of Abundance with KrakEN - title_md: bracken - - description_md: BUSCO assess genome and annotation completeness - title_md: busco - - description_md: Contig Annotation Tool (CAT) - title_md: cat - - description_md: simple tool for removing duplicates from sequencing reads - title_md: cd_hit_dup - - description_md: Cluster or compare biological sequence datasets - title_md: cdhit - - description_md: Gene co-expression network analysis tool - title_md: cemitool - - description_md: Assess the quality of microbial genomes recovered from isolates, - single cells, and metagenomes - title_md: checkm - - description_md: Symphonizing pileup and full-alignment for high-performance long-read - variant calling - title_md: clair3 - - description_md: 'NoD: a Nucleolar localization sequence detector for eukaryotic - and viral proteins' - title_md: clinod - - description_md: ClustalW multiple sequence alignment program for DNA or proteins - title_md: clustalw - - description_md: removes lower scoring overlaps from cmsearch results. - title_md: cmsearch_deoverlap - - description_md: Detects positive selection - title_md: codeml - - description_md: co-occurrence of mutations on amplicons - title_md: cojac - - description_md: Combine multiple Assemblystats datasets into a single tabular - report - title_md: combine_assembly_stats - - description_md: Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species - abundances and gene families/pathways abundances - title_md: combine_metaphlan_humann - - description_md: Compare outputs of HUMAnN2 for several samples and extract similar - and specific information - title_md: compare_humann2_output - - description_md: 'Compleasm: a faster and more accurate reimplementation of BUSCO' - title_md: compleasm - - description_md: 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. - title_md: concoct - - description_md: CoverM genome and contig wrappers - title_md: coverm - - description_md: CryptoGenotyper is a standalone tool to *in-silico* determine - species and subtype based on SSU rRNA and gp60 markers. - title_md: cryptogenotyper - - description_md: Flexible tool to remove adapter sequences (and quality trim) high - throughput sequencing reads (fasta/fastq). - title_md: cutadapt - - description_md: DADA2 wrappers - title_md: dada2 - - description_md: DAS Tool for genome resolved metagenomics - title_md: das_tool - - description_md: Differential gene expression analysis based on the negative binomial - distribution - title_md: deseq2 - - description_md: DIAMOND is a new alignment tool for aligning short DNA sequencing - reads to a protein reference database such as NCBI-NR. - title_md: diamond - - description_md: DISCO is a overlap-layout-consensus (OLC) metagenome assembler - title_md: disco - - description_md: DRAM for distilling microbial metabolism to automate the curation - of microbiome function - title_md: dram - - description_md: dRep compares and dereplicates genome sets - title_md: drep - - description_md: EC-Typer - in silico serotyping of Escherichia coli species - title_md: ectyper - - description_md: Find bacterial type III effectors in protein sequences - title_md: effectiveT3 - - description_md: eggnog-mapper fast functional annotation of novel sequences - title_md: eggnog_mapper - - description_md: Galaxy wrappers for EMBOSS version 5.0.0 tools - title_md: emboss_5 - - description_md: Analyse phylogenetic trees using the ETE Toolkit - title_md: ete - - description_md: export2graphlan is a conversion software tool for producing both - annotation and tree file for GraPhlAn - title_md: export2graphlan - - description_md: ggplot2 histograms and density plots - title_md: ez_histograms - - description_md: fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) - title_md: fargene - - description_md: Fast alignment-free computation of whole-genome Average Nucleotide - Identity - title_md: fastani - - description_md: 'FastK: A K-mer counter (for HQ assembly data sets)' - title_md: fastk - - description_md: Fast all-in-one preprocessing for FASTQ files - title_md: fastp - - description_md: FASTQE - title_md: fastqe - - description_md: FastTree infers approximately-maximum-likelihood phylogenetic - trees from alignments of nucleotide or protein sequences - GVL - title_md: fasttree - - description_md: featureCounts counts the number of reads aligned to defined masked - regions in a reference genome - title_md: featurecounts - - description_md: Remove short and repeat contigs/scaffolds - title_md: filter_spades_repeats - - description_md: Filtlong - Filtering long reads by quality - title_md: filtlong - - description_md: FlashLFQ mass-spectrometry proteomics label-free quantification - title_md: flashlfq - - description_md: Assembly of long and error-prone reads. - title_md: flye - - description_md: Format MetaPhlAn2 output to extract abundance at different taxonomic - levels - title_md: format_metaphlan2_output - - description_md: Tool for finding (fragmented) genes in short read - title_md: fraggenescan - - description_md: lineage abundances estimation - title_md: freyja - - description_md: Suite for metabarcoding analysis - title_md: frogs - - description_md: Funannotate is a genome prediction, annotation, and comparison - software package. - title_md: funannotate - - description_md: Download MLST datasets by species from pubmlst.org - title_md: getmlst - - description_md: 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. - title_md: ggplot2 - - description_md: Fetch taxonomic representation - title_md: gi2taxonomy - - description_md: Glimmer makes gene predictions. - title_md: glimmer - - description_md: GlimmerHMM is a new gene finder based on a Generalized Hidden - Markov Model (GHMM) - title_md: glimmer_hmm - - description_md: Performs GO Enrichment analysis. - title_md: goenrichment - - description_md: goseq does selection-unbiased testing for category enrichment - amongst differentially expressed (DE) genes for RNA-seq data - title_md: goseq - - description_md: GraPhlAn is a software tool for producing high-quality circular - representations of taxonomic and phylogenetic trees - title_md: graphlan - - description_md: Mapper for long, error-prone reads. - title_md: graphmap - - description_md: '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. ' - title_md: gtdbtk - - description_md: Gubbins - bacterial recombination detection - title_md: gubbins - - description_md: Convert AMR gene detection tool output to hAMRonization specification - format. - title_md: hamronization - - description_md: Heidelberg and Enteritidis SNP Elucidation - title_md: hansel - - description_md: A hifiasm fork for metagenome assembly using Hifi reads. - title_md: hifiasm_meta - - description_md: 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. - title_md: hivtrace - - description_md: 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). - title_md: hmmer3 - - description_md: HUMAnN for functionally profiling metagenomes and metatranscriptomes - at species-level resolution - title_md: humann - - description_md: Hypothesis Testing using Phylogenies - title_md: hyphy - - description_md: Super Fast & Accurate Polisher for Long Read Genome Assemblies - title_md: hypo - - description_md: ICEscreen identifies Integrative Conjugative Elements (ICEs) and - Integrative Mobilizable Elements (IMEs) in Bacillota genomes. - title_md: icescreen - - description_md: Wrappers for the idba assembler variants. - title_md: idba_ud - - description_md: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence - databases for RNA structure and sequence similarities. - title_md: infernal - - description_md: InStrain is a tool for analysis of co-occurring genome populations - from metagenomes - title_md: instrain - - description_md: '"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"' - title_md: integron_finder - - description_md: Interproscan queries the interpro database and provides annotations. - title_md: interproscan - - description_md: Interproscan queries the interpro database and provides annotations. - title_md: iprscan5 - - description_md: Efficient phylogenomic software by maximum likelihood - title_md: iqtree - - description_md: '"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."' - title_md: isescan - - description_md: ITSx is an open source software utility to extract the highly - variable ITS1 and ITS2 subregions from ITS sequences. - title_md: itsx - - description_md: iVar is a computational package that contains functions broadly - useful for viral amplicon-based sequencing - title_md: ivar - - description_md: JBrowse Genome Browser integrated as a Galaxy Tool - title_md: jbrowse - - description_md: Jellyfish is a tool for fast, memory-efficient counting of k-mers - in DNA - title_md: jellyfish - - description_md: Filtering kmers or reads from a database of kmers hashes - title_md: kat_filter - - description_md: Kc-Align custom tool - title_md: kc-align - - description_md: In-memory nucleotide sequence k-mer counting, filtering, graph - traversal and more - title_md: khmer - - description_md: Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella - pneumoniae species complex (KpSC) - title_md: kleborate - - description_md: Gene function annotation tool based on KEGG Orthology and hidden - Markov model - title_md: kofamscan - - description_md: 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. - title_md: kraken - - description_md: Kraken2 for taxonomic designation. - title_md: kraken2 - - description_md: Convert Kraken output to Galaxy taxonomy data. - title_md: kraken2tax - - description_md: Create BIOM-format tables (http://biom-format.org) from Kraken - output (http://ccb.jhu.edu/software/kraken/) - title_md: kraken_biom - - description_md: Kraken taxonomy report - title_md: kraken_taxonomy_report - - description_md: KrakenTools is a suite of scripts to be used alongside the Kraken - title_md: krakentools - - description_md: Predict MLST directly from uncorrected long reads - title_md: krocus - - description_md: Find lowest diagnostic rank - title_md: lca_wrapper - - description_md: Performs in silico Legionella pneumophila sequence based typing. - title_md: legsta - - description_md: Lighter is a kmer-based error correction method for whole genome - sequencing data - title_md: lighter - - description_md: Perform RNA-Seq differential expression analysis using limma voom - pipeline - title_md: limma_voom - - description_md: Identification of SARS-CoV-2 related metagenomic mutations based - on a single (or a list of) variant(s) file(s) - title_md: lineagespot - - description_md: Tools for M. tuberculosis DNA fingerprinting (spoligotyping) - title_md: lorikeet - - description_md: LotuS2 OTU processing pipeline - title_md: lotus2 - - description_md: m6anet to detect m6A RNA modifications from nanopore data - title_md: m6anet - - description_md: MaAsLin2 is comprehensive R package for efficiently determining - multivariable association between microbial meta'omic features and clinical - metadata. - title_md: maaslin2 - - description_md: Multiple alignment program for amino acid or nucleotide sequences - title_md: mafft - - description_md: Make a FASTA file non-redundant - title_md: make_nr - - description_md: 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. - title_md: maker - - description_md: fast and accurate sequence read classification tool designed to - assign taxonomy and OTU classifications to ribosomal RNA sequences. - title_md: mapseq - - description_md: Fast genome and metagenome distance estimation using MinHash - title_md: mash - - description_md: clusters metagenomic contigs into bins - title_md: maxbin2 - - description_md: wrapper for MaxQuant - title_md: maxquant - - description_md: The Markov Cluster Algorithm, a cluster algorithm for graphs - title_md: mcl - - description_md: Sequence correction provided by ONT Research - title_md: medaka - - description_md: An ultra-fast single-node solution for large and complex metagenomics - assembly via succinct de Bruijn graph. - title_md: megahit - - description_md: A subprogram within the Megahit toolkit for converting contigs - to assembly graphs (fastg) - title_md: megahit_contig2fastg - - description_md: 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). - title_md: megan - - description_md: Assign sequence type to N. meningitidis genome assemblies - title_md: meningotype - - description_md: Merqury is a tool for evaluating genomes assemblies based of k-mer - operations. - title_md: merqury - - description_md: Meryl a k-mer counter. - title_md: meryl - - description_md: 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. - title_md: metabat2 - - description_md: '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. ' - title_md: metaeuk - - description_md: MetaGeneAnnotator gene-finding program for prokaryote and phage - title_md: metagene_annotator - - description_md: metagenomeSeq Normalization - title_md: metagenomeseq - - description_md: Produce targeted databases for mass spectrometry analysis. - title_md: metanovo - - description_md: MetaPhlAn for Metagenomic Phylogenetic Analysis - title_md: metaphlan - - description_md: quantitative analysis of microbiome taxonomy and function - title_md: metaquantome - - description_md: A flexible pipeline for genome-resolved metagenomic data analysis - title_md: metawrapmg - - description_md: Short-read assembler based on a de Bruijn graph - title_md: minia - - description_md: Miniasm - Ultrafast de novo assembly for long noisy reads (though - having no consensus step) - title_md: miniasm - - description_md: Polishing miniasm assemblies - title_md: minipolish - - description_md: Align a protein sequence against a genome with affine gap penalty, - splicing and frameshift. - title_md: miniprot - - description_md: de-novo annotation of metazoan mitochondrial genomes - title_md: mitos - - description_md: Scan contig files against PubMLST typing schemes - title_md: mlst - - description_md: MOB-suite is a set of software tools for clustering, reconstruction - and typing of plasmids from draft assemblies - title_md: mob_suite - - description_md: Mothur wrappers - title_md: mothur - - description_md: A program for the Bayesian estimation of phylogeny. - title_md: mrbayes - - description_md: msconvert Convert and/or filter mass spectrometry files (including - vendor formats) using the official Docker container - title_md: msconvert - - description_md: MSstatsTMT protein significance analysis in shotgun mass spectrometry-based - proteomic experiments with tandem mass tag (TMT) labeling - title_md: msstatstmt - - description_md: GSEA-based pathway enrichment analysis for multi-omics data - title_md: multigsea - - description_md: MultiQC aggregates results from bioinformatics analyses across - many samples into a single report - title_md: multiqc - - description_md: Antibiotic resistance predictions - title_md: mykrobe - - description_md: RScript to parse the results of mykrobe predictor. - title_md: mykrobe_parser - - description_md: Creates a SQLite database for proteomics data - title_md: mz_to_sqlite - - description_md: 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. - title_md: nanocompore - - description_md: Plotting tool for long read sequencing data and alignments - title_md: nanoplot - - description_md: 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. - title_md: nanopolishcomp - - description_md: NCBI BLAST+ - title_md: ncbi_blast_plus - - description_md: FCS-GX detects contamination from foreign organisms in genome - sequences using the genome cross-species aligner (GX). - title_md: ncbi_fcs_gx - - description_md: Perform operations on Newick trees - title_md: newick_utils - - description_md: Identify differences between your sequences and a reference sequence - used by Nextstrain - title_md: nextclade - - description_md: String graph-based de novo assembler for long reads - title_md: nextdenovo - - description_md: Estimate average coverage in metagenomic datasets - title_md: nonpareil - - description_md: Prediction of Nucleosomes Positions on the Genome - title_md: nucleosome_prediction - - description_md: Marks/removes PCR introduced duplicate molecules based on the - molecular tagging technology used in NuGEN products. - title_md: nugen_nudup - - description_md: Compute biodiveristy indicators for marine data from obis - title_md: obisindicators - - description_md: OBITools is a set of programs developed to simplify the manipulation - of sequence files - title_md: obitools - - description_md: Proteome quality assessment software - title_md: omark - - description_md: Galaxy wrapper for ORFIPY - title_md: orfipy - - description_md: Accurate inference of orthologous gene groups made easy - title_md: orthofinder - - description_md: PeptideShaker and SearchGUI - title_md: peptideshaker - - description_md: Search a FASTA sequence against a library of Pfam HMM. - title_md: pfamscan - - description_md: rapid standardised annotation tool for bacteriophage genomes and - metagenomes - title_md: pharokka - - description_md: Handling and analysis of high-throughput microbiome census data - title_md: phyloseq - - description_md: PhyML is a phylogeny software based on the maximum-likelihood - principle. - title_md: phyml - - description_md: PICRUSt wrappers - title_md: picrust - - description_md: 'PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction - of Unobserved States' - title_md: picrust2 - - description_md: PlasFlow - Prediction of plasmid sequences in metagenomic contigs. - title_md: plasflow - - description_md: '"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"' - title_md: plasmidfinder - - description_md: Genome assembler for assemblying plasmid - title_md: plasmidspades - - description_md: '"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."' - title_md: polypolish - - description_md: A protein-coding gene prediction software tool for bacterial and - archaeal genomes - title_md: prodigal - - description_md: Rapid annotation of prokaryotic genomes - title_md: prokka - - description_md: Aligns two sets of contigs and reports amino acid substitutions - between them - title_md: promer - - description_md: Proteinortho is a tool to detect orthologous proteins/genes within - different species. - title_md: proteinortho - - description_md: QC metrics for ONT Basecalling - title_md: pycoqc - - description_md: 'pyGenomeTracks: Standalone program and library to plot beautiful - genome browser tracks.' - title_md: pygenometracks - - description_md: QIIME to perform microbial community analysis - title_md: qiime_add_on - - description_md: QIIME to perform microbial community analysis - title_md: qiime_core - - description_md: 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. - title_md: qualimap - - description_md: Quast (Quality ASsessment Tool) evaluates genome assemblies. - title_md: quast - - description_md: Merge long-read and hybrid assemblies to increase contiguity - title_md: quickmerge - - description_md: Identification of ribosomal RNA genes in metagenomic fragments. - title_md: rRNA - - description_md: Consensus module for raw de novo DNA assembly of long uncorrected - reads. - title_md: racon - - description_md: Randomly subsample sequencing reads to a specified coverage - title_md: rasusa - - description_md: RAxML - A Maximum Likelihood based phylogenetic inference - title_md: raxml - - description_md: Rapid decontamination of SARS-CoV-2 sequencing reads - title_md: read_it_and_keep - - description_md: Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic - data. - title_md: reago - - description_md: '"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."' - title_md: recentrifuge - - description_md: Tool for annotation of repeats from unassembled shotgun reads. - title_md: repeatexplorer2 - - description_md: Roary the pangenome pipeline - title_md: roary - - description_md: an RNA-seq quality control package - title_md: rseqc - - description_md: Salmon is a wicked-fast program to produce a highly-accurate, - transcript-level quantification estimates from RNA-seq and single-cell data. - title_md: salmon - - description_md: sarscov2formatter custom script - title_md: sarscov2formatter - - description_md: sarscov2summary custom script - title_md: sarscov2summary - - description_md: Scoary calculates the assocations between all genes in the accessory - genome and the traits. - title_md: scoary - - description_md: 'SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural - Networks' - title_md: semibin - - description_md: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation - title_md: seqkit - - description_md: Tool for merging paired-end Illumina reads and trimming adapters. - title_md: seqprep - - description_md: Salmonella serotype prediction from genome sequencing data - title_md: seqsero2 - - description_md: Reconstruct haplotypes using ShoRAH in amplicon mode - title_md: shorah - - description_md: Faster de novo assembly pipeline based around Spades - title_md: shovill - - description_md: SISTR in silico serotyping tool - title_md: sistr_cmd - - description_md: Set of utilities for manipulating small viral genome data. - title_md: smallgenomeutilities - - description_md: SMALT aligns DNA sequencing reads with a reference genome. - title_md: smalt - - description_md: SNAP is a general purpose gene finding program suitable for both - eukaryotic and prokaryotic genomes. - title_md: snap - - description_md: Contains the snippy tool for characterising microbial snps - title_md: snippy - - description_md: Scripts for parsing Mykrobe predict results for Shigella sonnei. - title_md: sonneityping - - description_md: SortMeRNA is a software designed to rapidly filter ribosomal RNA - fragments from metatransriptomic data produced by next-generation sequencers. - title_md: sortmerna - - description_md: '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.' - title_md: spades - - description_md: SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping - from sequence reads - title_md: spotyping - - description_md: bowtie wrapper tool to align small RNA sequencing reads - title_md: sr_bowtie - - description_md: Short Read Sequence Typing for Bacterial Pathogens - title_md: srst2 - - description_md: SRST2 Short Read Sequence Typing for Bacterial Pathogens - title_md: srst2 - - description_md: Scan genome contigs against the ResFinder, PlasmidFinder, and - PointFinder antimicrobial resistance databases. - title_md: staramr - - description_md: Rapid and accurate identification of the sequence type (ST) - title_md: stringmlst - - description_md: for using multi-locus genotype data to investigate population - structure. - title_md: structure - - description_md: .nan - title_md: suite_qiime2__alignment - - description_md: .nan - title_md: suite_qiime2__composition - - description_md: .nan - title_md: suite_qiime2__cutadapt - - description_md: .nan - title_md: suite_qiime2__dada2 - - description_md: .nan - title_md: suite_qiime2__deblur - - description_md: .nan - title_md: suite_qiime2__demux - - description_md: .nan - title_md: suite_qiime2__diversity - - description_md: .nan - title_md: suite_qiime2__diversity_lib - - description_md: .nan - title_md: suite_qiime2__emperor - - description_md: .nan - title_md: suite_qiime2__feature_classifier - - description_md: .nan - title_md: suite_qiime2__feature_table - - description_md: .nan - title_md: suite_qiime2__fragment_insertion - - description_md: .nan - title_md: suite_qiime2__longitudinal - - description_md: .nan - title_md: suite_qiime2__metadata - - description_md: .nan - title_md: suite_qiime2__phylogeny - - description_md: .nan - title_md: suite_qiime2__quality_control - - description_md: .nan - title_md: suite_qiime2__quality_filter - - description_md: .nan - title_md: suite_qiime2__rescript - - description_md: .nan - title_md: suite_qiime2__sample_classifier - - description_md: .nan - title_md: suite_qiime2__taxa - - description_md: .nan - title_md: suite_qiime2__vsearch - - description_md: .nan - title_md: suite_qiime2_core - - description_md: .nan - title_md: suite_qiime2_core__tools - - description_md: Draw phylogeny - title_md: t2ps - - description_md: Summarize taxonomy - title_md: t2t_report - - description_md: T-Coffee - title_md: t_coffee - - description_md: Krona pie chart from taxonomic profile - title_md: taxonomy_krona_chart - - description_md: Processes M. tuberculosis sequence data to infer strain type and - identify known drug resistance markers. - title_md: tb-profiler - - description_md: ToolDistillator extract and aggregate information from different - tool outputs to JSON parsable files - title_md: tooldistillator - - description_md: TRANSIT - title_md: transit - - description_md: Finds rho-independent transcription terminators in bacterial genomes - title_md: transtermhp - - description_md: Trim Galore adaptive quality and adapter trimmer - title_md: trim_galore - - description_md: Trycycler toolkit wrappers - title_md: trycycler - - description_md: Unicycler is a hybrid assembly pipeline for bacterial genomes. - title_md: unicycler - - description_md: Unipept retrieves metaproteomics information - title_md: unipept - - description_md: Download UniProt proteome in XML or fasta format - title_md: uniprotxml_downloader - - description_md: UShER toolkit wrappers - title_md: usher - - description_md: A pipeline for detecting mis-assemblies in metagenomic assemblies. - title_md: valet - - description_md: Classify Influenza samples from raw short read sequence data - title_md: vapor - - description_md: Variable VirusAMPlicons (varVAMP) is a tool to design primers - for highly diverse viruses - title_md: varvamp - - description_md: an R package fo community ecologist - title_md: vegan - - description_md: de novo genomic assembler specially designed for short read sequencing - technologies - title_md: velvet - - description_md: Automatically optimize Velvet assemblies - title_md: velvet_optimiser - - description_md: virAnnot wrappers - title_md: virAnnot - - description_md: VSEARCH including searching, clustering, chimera detection, dereplication, - sorting, masking and shuffling of sequences. - title_md: vsearch - - description_md: WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads - assembly. - title_md: wtdbg - id: tool_list +- id: tool_list title: List of community curated tools available for microGalaxy -title: Community Tools + content: + - title_md: PAMPA + description_md: Tools to compute and analyse biodiversity metrics + - title_md: TreeBest + description_md: TreeBeST best + - title_md: abacas + description_md: Order and Orientate Contigs + - title_md: abricate + description_md: Mass screening of contigs for antiobiotic resistance genes From e6ca5a302d3be8fa0a9e0eb745705e072d7a7f41 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 16:36:28 +0100 Subject: [PATCH 14/38] remote tools --- communities/microgalaxy/lab/base.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index f48401be..5a1f1be7 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -64,6 +64,6 @@ sections: - sections/1_beginner.yml - sections/3_advanced.yml - sections/4_community.yml - - sections/5_tools.yml + # - sections/5_tools.yml # ----------------------------------------------------------------------------- From b42d0716a230e0f358f6d4080cedcbc79473e0d1 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 16:38:59 +0100 Subject: [PATCH 15/38] test --- communities/microgalaxy/lab/base.yml | 2 +- .../microgalaxy/lab/sections/5_tools.yml | 9 +-- .../resources/.~lock.curated_tools.tsv# | 1 + sources/bin/populate_labs.py | 70 +++++++++++++++++++ 4 files changed, 74 insertions(+), 8 deletions(-) create mode 100644 communities/microgalaxy/resources/.~lock.curated_tools.tsv# create mode 100644 sources/bin/populate_labs.py diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index 5a1f1be7..f48401be 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -64,6 +64,6 @@ sections: - sections/1_beginner.yml - sections/3_advanced.yml - sections/4_community.yml - # - sections/5_tools.yml + - sections/5_tools.yml # ----------------------------------------------------------------------------- diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 11a75ac8..323d36c2 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -5,10 +5,5 @@ tabs: title: List of community curated tools available for microGalaxy content: - title_md: PAMPA - description_md: Tools to compute and analyse biodiversity metrics - - title_md: TreeBest - description_md: TreeBeST best - - title_md: abacas - description_md: Order and Orientate Contigs - - title_md: abricate - description_md: Mass screening of contigs for antiobiotic resistance genes + description_md: > + Tools to compute and analyse biodiversity metrics diff --git a/communities/microgalaxy/resources/.~lock.curated_tools.tsv# b/communities/microgalaxy/resources/.~lock.curated_tools.tsv# new file mode 100644 index 00000000..b540fde2 --- /dev/null +++ b/communities/microgalaxy/resources/.~lock.curated_tools.tsv# @@ -0,0 +1 @@ +,paul,paul-LIFEBOOK-U7410,07.11.2024 12:25,file:///home/paul/.config/libreoffice/4; \ No newline at end of file diff --git a/sources/bin/populate_labs.py b/sources/bin/populate_labs.py new file mode 100644 index 00000000..6e28ce12 --- /dev/null +++ b/sources/bin/populate_labs.py @@ -0,0 +1,70 @@ +import argparse +import os +from typing import List + +import oyaml as yaml +import pandas as pd + +# import yaml + + +def main() -> None: + parser = argparse.ArgumentParser(description="Create community tools.yml from tool.tsv.") + + # Adding positional arguments with short options + parser.add_argument( + "-c", "--tool_tsv", type=str, required=True, help="Path to the TSV file (e.g., curated_tools.tsv)" + ) + parser.add_argument( + "-y", "--tool_yml", type=str, required=True, help="Path to the output YAML file (e.g., tools.yml)" + ) + + args = parser.parse_args() + + # Check if the tool TSV file exists + if not os.path.exists(args.tool_tsv): + print(f"Error: The file '{args.tool_tsv}' does not exist.") + return + + try: + # Read the TSV file with pandas (use tab delimiter) + data = pd.read_csv(args.tool_tsv, sep="\t") + + # Construct the YAML data structure + yaml_data = { + "id": "tools", + "title": "Community Tools", + "tabs": [ + {"id": "tool_list", "title": "List of community curated tools available for microGalaxy", "content": []} + ], + } + + # Populate the content section with each row from the TSV + for _, row in data.iterrows(): + # Use the first column (assumed to be the tool title) as the title_md + title_md = row[data.columns[0]] # Get the first column's value as title_md + + # Start the unordered list
    and construct each
  • for every other column in the row + description = row["Description"] + # for column in data.columns[1:]: # Skip the first column (since it's title_md) + # description += f"
  • {column}: {row[column]}
    • \n" + # description += "
" + + # Create the tool entry with the formatted HTML list + tool_entry = { + "title_md": title_md, + "description_md": description, # Directly insert the HTML string without escape sequences + } + yaml_data["tabs"][0]["content"].append(tool_entry) + + # Write the YAML data to the output file + with open(args.tool_yml, "w") as yaml_file: + yaml.dump(yaml_data, yaml_file, default_flow_style=False, allow_unicode=True, indent=2) + print(f"Data successfully written to '{args.tool_yml}'") + + except Exception as e: + print(f"An error occurred: {e}") + + +if __name__ == "__main__": + main() From be900c90f4b608a8d93a63c40e406dd56ce64455 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 17:12:57 +0100 Subject: [PATCH 16/38] test --- communities/microgalaxy/lab/sections/5_tools.yml | 12 ++++++------ sources/bin/populate_labs.py | 8 ++++---- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 323d36c2..b3f240da 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -1,9 +1,9 @@ id: tools title: Community Tools tabs: -- id: tool_list - title: List of community curated tools available for microGalaxy - content: - - title_md: PAMPA - description_md: > - Tools to compute and analyse biodiversity metrics + - id: tool_list + title: List of community curated tools available for microGalaxy + content: + - title_md: PAMPA + description_md: > + Tools to compute and analyse biodiversity metrics diff --git a/sources/bin/populate_labs.py b/sources/bin/populate_labs.py index 6e28ce12..b08b7a8f 100644 --- a/sources/bin/populate_labs.py +++ b/sources/bin/populate_labs.py @@ -45,10 +45,10 @@ def main() -> None: title_md = row[data.columns[0]] # Get the first column's value as title_md # Start the unordered list
    and construct each
  • for every other column in the row - description = row["Description"] - # for column in data.columns[1:]: # Skip the first column (since it's title_md) - # description += f"
  • {column}: {row[column]}
    • \n" - # description += "
" + description = "
    " + for column in data.columns[1:]: # Skip the first column (since it's title_md) + description += f"
  • {column}: {row[column]}
    • \n" + description += "
" # Create the tool entry with the formatted HTML list tool_entry = { From 5b6d0fa672f519c3960ab29ae7bf71dc222591e7 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 17:14:56 +0100 Subject: [PATCH 17/38] test --- .../microgalaxy/lab/sections/5_tools.yml | 747 +++++++++++++++++- sources/bin/populate_labs.py | 8 +- 2 files changed, 745 insertions(+), 10 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index b3f240da..3318efec 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -1,9 +1,744 @@ id: tools title: Community Tools tabs: - - id: tool_list - title: List of community curated tools available for microGalaxy - content: - - title_md: PAMPA - description_md: > - Tools to compute and analyse biodiversity metrics +- id: tool_list + title: List of community curated tools available for microGalaxy + content: + - title_md: PAMPA + description_md: Tools to compute and analyse biodiversity metrics + - title_md: TreeBest + description_md: TreeBeST best + - title_md: abacas + description_md: Order and Orientate Contigs + - title_md: abricate + description_md: Mass screening of contigs for antiobiotic resistance genes + - title_md: abritamr + description_md: A pipeline for running AMRfinderPlus and collating results into + functional classes + - title_md: abyss + description_md: Assembly By Short Sequences - a de novo, parallel, paired-end + sequence assembler + - title_md: aldex2 + description_md: Performs analysis Of differential abundance taking sample variation + into account + - title_md: amplican + description_md: AmpliCan is an analysis tool for genome editing. + - title_md: amrfinderplus + description_md: '"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.' + - title_md: ancombc + description_md: Performs analysis of compositions of microbiomes with bias correction. + - title_md: antismash + description_md: Antismash allows the genome-wide identification, annotation and + analysis of secondary metabolite biosynthesis gene clusters + - title_md: artic + description_md: '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' + - title_md: assemblystats + description_md: Summarise an assembly (e.g. N50 metrics) + - title_md: bakta + description_md: '"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."' + - title_md: bamtools + description_md: Operate on and transform BAM datasets in various ways using bamtools + - title_md: bandage + description_md: Bandage - A Bioinformatics Application for Navigating De novo + Assembly Graphs Easily + - title_md: bayescan + description_md: Detecting natural selection from population-based genetic data + - title_md: bbtools + description_md: 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. + - title_md: bigscape + description_md: Construct sequence similarity networks of BGCs and groups them + into GCF + - title_md: binning_refiner + description_md: Reconciles the outputs of different binning programs with the + aim to improve the quality of genome bins,especially with respect to contamination + levels. + - title_md: biohansel + description_md: Heidelberg and Enteritidis SNP Elucidation + - title_md: biom_format + description_md: The biom-format package provides a command line interface and + Python API for working with BIOM files. + - title_md: biotradis + description_md: Bio-Tradis is a tool suite dedicated to essentiality analyses + with TraDis data. + - title_md: blast2go + description_md: Maps BLAST results to GO annotation terms + - title_md: blast_rbh + description_md: BLAST Reciprocal Best Hits (RBH) from two FASTA files + - title_md: blastxml_to_top_descr + description_md: Make table of top BLAST match descriptions + - title_md: bracken + description_md: Bayesian Reestimation of Abundance with KrakEN + - title_md: busco + description_md: BUSCO assess genome and annotation completeness + - title_md: cat + description_md: Contig Annotation Tool (CAT) + - title_md: cd_hit_dup + description_md: simple tool for removing duplicates from sequencing reads + - title_md: cdhit + description_md: Cluster or compare biological sequence datasets + - title_md: cemitool + description_md: Gene co-expression network analysis tool + - title_md: checkm + description_md: Assess the quality of microbial genomes recovered from isolates, + single cells, and metagenomes + - title_md: clair3 + description_md: Symphonizing pileup and full-alignment for high-performance long-read + variant calling + - title_md: clinod + description_md: 'NoD: a Nucleolar localization sequence detector for eukaryotic + and viral proteins' + - title_md: clustalw + description_md: ClustalW multiple sequence alignment program for DNA or proteins + - title_md: cmsearch_deoverlap + description_md: removes lower scoring overlaps from cmsearch results. + - title_md: codeml + description_md: Detects positive selection + - title_md: cojac + description_md: co-occurrence of mutations on amplicons + - title_md: combine_assembly_stats + description_md: Combine multiple Assemblystats datasets into a single tabular + report + - title_md: combine_metaphlan_humann + description_md: Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species + abundances and gene families/pathways abundances + - title_md: compare_humann2_output + description_md: Compare outputs of HUMAnN2 for several samples and extract similar + and specific information + - title_md: compleasm + description_md: 'Compleasm: a faster and more accurate reimplementation of BUSCO' + - title_md: concoct + description_md: 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. + - title_md: coverm + description_md: CoverM genome and contig wrappers + - title_md: cryptogenotyper + description_md: CryptoGenotyper is a standalone tool to *in-silico* determine + species and subtype based on SSU rRNA and gp60 markers. + - title_md: cutadapt + description_md: Flexible tool to remove adapter sequences (and quality trim) high + throughput sequencing reads (fasta/fastq). + - title_md: dada2 + description_md: DADA2 wrappers + - title_md: das_tool + description_md: DAS Tool for genome resolved metagenomics + - title_md: deseq2 + description_md: Differential gene expression analysis based on the negative binomial + distribution + - title_md: diamond + description_md: DIAMOND is a new alignment tool for aligning short DNA sequencing + reads to a protein reference database such as NCBI-NR. + - title_md: disco + description_md: DISCO is a overlap-layout-consensus (OLC) metagenome assembler + - title_md: dram + description_md: DRAM for distilling microbial metabolism to automate the curation + of microbiome function + - title_md: drep + description_md: dRep compares and dereplicates genome sets + - title_md: ectyper + description_md: EC-Typer - in silico serotyping of Escherichia coli species + - title_md: effectiveT3 + description_md: Find bacterial type III effectors in protein sequences + - title_md: eggnog_mapper + description_md: eggnog-mapper fast functional annotation of novel sequences + - title_md: emboss_5 + description_md: Galaxy wrappers for EMBOSS version 5.0.0 tools + - title_md: ete + description_md: Analyse phylogenetic trees using the ETE Toolkit + - title_md: export2graphlan + description_md: export2graphlan is a conversion software tool for producing both + annotation and tree file for GraPhlAn + - title_md: ez_histograms + description_md: ggplot2 histograms and density plots + - title_md: fargene + description_md: fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) + - title_md: fastani + description_md: Fast alignment-free computation of whole-genome Average Nucleotide + Identity + - title_md: fastk + description_md: 'FastK: A K-mer counter (for HQ assembly data sets)' + - title_md: fastp + description_md: Fast all-in-one preprocessing for FASTQ files + - title_md: fastqe + description_md: FASTQE + - title_md: fasttree + description_md: FastTree infers approximately-maximum-likelihood phylogenetic + trees from alignments of nucleotide or protein sequences - GVL + - title_md: featurecounts + description_md: featureCounts counts the number of reads aligned to defined masked + regions in a reference genome + - title_md: filter_spades_repeats + description_md: Remove short and repeat contigs/scaffolds + - title_md: filtlong + description_md: Filtlong - Filtering long reads by quality + - title_md: flashlfq + description_md: FlashLFQ mass-spectrometry proteomics label-free quantification + - title_md: flye + description_md: Assembly of long and error-prone reads. + - title_md: format_metaphlan2_output + description_md: Format MetaPhlAn2 output to extract abundance at different taxonomic + levels + - title_md: fraggenescan + description_md: Tool for finding (fragmented) genes in short read + - title_md: freyja + description_md: lineage abundances estimation + - title_md: frogs + description_md: Suite for metabarcoding analysis + - title_md: funannotate + description_md: Funannotate is a genome prediction, annotation, and comparison + software package. + - title_md: getmlst + description_md: Download MLST datasets by species from pubmlst.org + - title_md: ggplot2 + description_md: 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. + - title_md: gi2taxonomy + description_md: Fetch taxonomic representation + - title_md: glimmer + description_md: Glimmer makes gene predictions. + - title_md: glimmer_hmm + description_md: GlimmerHMM is a new gene finder based on a Generalized Hidden + Markov Model (GHMM) + - title_md: goenrichment + description_md: Performs GO Enrichment analysis. + - title_md: goseq + description_md: goseq does selection-unbiased testing for category enrichment + amongst differentially expressed (DE) genes for RNA-seq data + - title_md: graphlan + description_md: GraPhlAn is a software tool for producing high-quality circular + representations of taxonomic and phylogenetic trees + - title_md: graphmap + description_md: Mapper for long, error-prone reads. + - title_md: gtdbtk + description_md: '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. ' + - title_md: gubbins + description_md: Gubbins - bacterial recombination detection + - title_md: hamronization + description_md: Convert AMR gene detection tool output to hAMRonization specification + format. + - title_md: hansel + description_md: Heidelberg and Enteritidis SNP Elucidation + - title_md: hifiasm_meta + description_md: A hifiasm fork for metagenome assembly using Hifi reads. + - title_md: hivtrace + description_md: 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. + - title_md: hmmer3 + description_md: 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). + - title_md: humann + description_md: HUMAnN for functionally profiling metagenomes and metatranscriptomes + at species-level resolution + - title_md: hyphy + description_md: Hypothesis Testing using Phylogenies + - title_md: hypo + description_md: Super Fast & Accurate Polisher for Long Read Genome Assemblies + - title_md: icescreen + description_md: ICEscreen identifies Integrative Conjugative Elements (ICEs) and + Integrative Mobilizable Elements (IMEs) in Bacillota genomes. + - title_md: idba_ud + description_md: Wrappers for the idba assembler variants. + - title_md: infernal + description_md: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence + databases for RNA structure and sequence similarities. + - title_md: instrain + description_md: InStrain is a tool for analysis of co-occurring genome populations + from metagenomes + - title_md: integron_finder + description_md: '"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"' + - title_md: interproscan + description_md: Interproscan queries the interpro database and provides annotations. + - title_md: iprscan5 + description_md: Interproscan queries the interpro database and provides annotations. + - title_md: iqtree + description_md: Efficient phylogenomic software by maximum likelihood + - title_md: isescan + description_md: '"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."' + - title_md: itsx + description_md: ITSx is an open source software utility to extract the highly + variable ITS1 and ITS2 subregions from ITS sequences. + - title_md: ivar + description_md: iVar is a computational package that contains functions broadly + useful for viral amplicon-based sequencing + - title_md: jbrowse + description_md: JBrowse Genome Browser integrated as a Galaxy Tool + - title_md: jellyfish + description_md: Jellyfish is a tool for fast, memory-efficient counting of k-mers + in DNA + - title_md: kat_filter + description_md: Filtering kmers or reads from a database of kmers hashes + - title_md: kc-align + description_md: Kc-Align custom tool + - title_md: khmer + description_md: In-memory nucleotide sequence k-mer counting, filtering, graph + traversal and more + - title_md: kleborate + description_md: Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella + pneumoniae species complex (KpSC) + - title_md: kofamscan + description_md: Gene function annotation tool based on KEGG Orthology and hidden + Markov model + - title_md: kraken + description_md: 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. + - title_md: kraken2 + description_md: Kraken2 for taxonomic designation. + - title_md: kraken2tax + description_md: Convert Kraken output to Galaxy taxonomy data. + - title_md: kraken_biom + description_md: Create BIOM-format tables (http://biom-format.org) from Kraken + output (http://ccb.jhu.edu/software/kraken/) + - title_md: kraken_taxonomy_report + description_md: Kraken taxonomy report + - title_md: krakentools + description_md: KrakenTools is a suite of scripts to be used alongside the Kraken + - title_md: krocus + description_md: Predict MLST directly from uncorrected long reads + - title_md: lca_wrapper + description_md: Find lowest diagnostic rank + - title_md: legsta + description_md: Performs in silico Legionella pneumophila sequence based typing. + - title_md: lighter + description_md: Lighter is a kmer-based error correction method for whole genome + sequencing data + - title_md: limma_voom + description_md: Perform RNA-Seq differential expression analysis using limma voom + pipeline + - title_md: lineagespot + description_md: Identification of SARS-CoV-2 related metagenomic mutations based + on a single (or a list of) variant(s) file(s) + - title_md: lorikeet + description_md: Tools for M. tuberculosis DNA fingerprinting (spoligotyping) + - title_md: lotus2 + description_md: LotuS2 OTU processing pipeline + - title_md: m6anet + description_md: m6anet to detect m6A RNA modifications from nanopore data + - title_md: maaslin2 + description_md: MaAsLin2 is comprehensive R package for efficiently determining + multivariable association between microbial meta'omic features and clinical + metadata. + - title_md: mafft + description_md: Multiple alignment program for amino acid or nucleotide sequences + - title_md: make_nr + description_md: Make a FASTA file non-redundant + - title_md: maker + description_md: 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. + - title_md: mapseq + description_md: fast and accurate sequence read classification tool designed to + assign taxonomy and OTU classifications to ribosomal RNA sequences. + - title_md: mash + description_md: Fast genome and metagenome distance estimation using MinHash + - title_md: maxbin2 + description_md: clusters metagenomic contigs into bins + - title_md: maxquant + description_md: wrapper for MaxQuant + - title_md: mcl + description_md: The Markov Cluster Algorithm, a cluster algorithm for graphs + - title_md: medaka + description_md: Sequence correction provided by ONT Research + - title_md: megahit + description_md: An ultra-fast single-node solution for large and complex metagenomics + assembly via succinct de Bruijn graph. + - title_md: megahit_contig2fastg + description_md: A subprogram within the Megahit toolkit for converting contigs + to assembly graphs (fastg) + - title_md: megan + description_md: 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). + - title_md: meningotype + description_md: Assign sequence type to N. meningitidis genome assemblies + - title_md: merqury + description_md: Merqury is a tool for evaluating genomes assemblies based of k-mer + operations. + - title_md: meryl + description_md: Meryl a k-mer counter. + - title_md: metabat2 + description_md: 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. + - title_md: metaeuk + description_md: '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. ' + - title_md: metagene_annotator + description_md: MetaGeneAnnotator gene-finding program for prokaryote and phage + - title_md: metagenomeseq + description_md: metagenomeSeq Normalization + - title_md: metanovo + description_md: Produce targeted databases for mass spectrometry analysis. + - title_md: metaphlan + description_md: MetaPhlAn for Metagenomic Phylogenetic Analysis + - title_md: metaquantome + description_md: quantitative analysis of microbiome taxonomy and function + - title_md: metawrapmg + description_md: A flexible pipeline for genome-resolved metagenomic data analysis + - title_md: minia + description_md: Short-read assembler based on a de Bruijn graph + - title_md: miniasm + description_md: Miniasm - Ultrafast de novo assembly for long noisy reads (though + having no consensus step) + - title_md: minipolish + description_md: Polishing miniasm assemblies + - title_md: miniprot + description_md: Align a protein sequence against a genome with affine gap penalty, + splicing and frameshift. + - title_md: mitos + description_md: de-novo annotation of metazoan mitochondrial genomes + - title_md: mlst + description_md: Scan contig files against PubMLST typing schemes + - title_md: mob_suite + description_md: MOB-suite is a set of software tools for clustering, reconstruction + and typing of plasmids from draft assemblies + - title_md: mothur + description_md: Mothur wrappers + - title_md: mrbayes + description_md: A program for the Bayesian estimation of phylogeny. + - title_md: msconvert + description_md: msconvert Convert and/or filter mass spectrometry files (including + vendor formats) using the official Docker container + - title_md: msstatstmt + description_md: MSstatsTMT protein significance analysis in shotgun mass spectrometry-based + proteomic experiments with tandem mass tag (TMT) labeling + - title_md: multigsea + description_md: GSEA-based pathway enrichment analysis for multi-omics data + - title_md: multiqc + description_md: MultiQC aggregates results from bioinformatics analyses across + many samples into a single report + - title_md: mykrobe + description_md: Antibiotic resistance predictions + - title_md: mykrobe_parser + description_md: RScript to parse the results of mykrobe predictor. + - title_md: mz_to_sqlite + description_md: Creates a SQLite database for proteomics data + - title_md: nanocompore + description_md: 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. + - title_md: nanoplot + description_md: Plotting tool for long read sequencing data and alignments + - title_md: nanopolishcomp + description_md: 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. + - title_md: ncbi_blast_plus + description_md: NCBI BLAST+ + - title_md: ncbi_fcs_gx + description_md: FCS-GX detects contamination from foreign organisms in genome + sequences using the genome cross-species aligner (GX). + - title_md: newick_utils + description_md: Perform operations on Newick trees + - title_md: nextclade + description_md: Identify differences between your sequences and a reference sequence + used by Nextstrain + - title_md: nextdenovo + description_md: String graph-based de novo assembler for long reads + - title_md: nonpareil + description_md: Estimate average coverage in metagenomic datasets + - title_md: nucleosome_prediction + description_md: Prediction of Nucleosomes Positions on the Genome + - title_md: nugen_nudup + description_md: Marks/removes PCR introduced duplicate molecules based on the + molecular tagging technology used in NuGEN products. + - title_md: obisindicators + description_md: Compute biodiveristy indicators for marine data from obis + - title_md: obitools + description_md: OBITools is a set of programs developed to simplify the manipulation + of sequence files + - title_md: omark + description_md: Proteome quality assessment software + - title_md: orfipy + description_md: Galaxy wrapper for ORFIPY + - title_md: orthofinder + description_md: Accurate inference of orthologous gene groups made easy + - title_md: peptideshaker + description_md: PeptideShaker and SearchGUI + - title_md: pfamscan + description_md: Search a FASTA sequence against a library of Pfam HMM. + - title_md: pharokka + description_md: rapid standardised annotation tool for bacteriophage genomes and + metagenomes + - title_md: phyloseq + description_md: Handling and analysis of high-throughput microbiome census data + - title_md: phyml + description_md: PhyML is a phylogeny software based on the maximum-likelihood + principle. + - title_md: picrust + description_md: PICRUSt wrappers + - title_md: picrust2 + description_md: 'PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction + of Unobserved States' + - title_md: plasflow + description_md: PlasFlow - Prediction of plasmid sequences in metagenomic contigs. + - title_md: plasmidfinder + description_md: '"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"' + - title_md: plasmidspades + description_md: Genome assembler for assemblying plasmid + - title_md: polypolish + description_md: '"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."' + - title_md: prodigal + description_md: A protein-coding gene prediction software tool for bacterial and + archaeal genomes + - title_md: prokka + description_md: Rapid annotation of prokaryotic genomes + - title_md: promer + description_md: Aligns two sets of contigs and reports amino acid substitutions + between them + - title_md: proteinortho + description_md: Proteinortho is a tool to detect orthologous proteins/genes within + different species. + - title_md: pycoqc + description_md: QC metrics for ONT Basecalling + - title_md: pygenometracks + description_md: 'pyGenomeTracks: Standalone program and library to plot beautiful + genome browser tracks.' + - title_md: qiime_add_on + description_md: QIIME to perform microbial community analysis + - title_md: qiime_core + description_md: QIIME to perform microbial community analysis + - title_md: qualimap + description_md: 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. + - title_md: quast + description_md: Quast (Quality ASsessment Tool) evaluates genome assemblies. + - title_md: quickmerge + description_md: Merge long-read and hybrid assemblies to increase contiguity + - title_md: rRNA + description_md: Identification of ribosomal RNA genes in metagenomic fragments. + - title_md: racon + description_md: Consensus module for raw de novo DNA assembly of long uncorrected + reads. + - title_md: rasusa + description_md: Randomly subsample sequencing reads to a specified coverage + - title_md: raxml + description_md: RAxML - A Maximum Likelihood based phylogenetic inference + - title_md: read_it_and_keep + description_md: Rapid decontamination of SARS-CoV-2 sequencing reads + - title_md: reago + description_md: Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic + data. + - title_md: recentrifuge + description_md: '"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."' + - title_md: repeatexplorer2 + description_md: Tool for annotation of repeats from unassembled shotgun reads. + - title_md: roary + description_md: Roary the pangenome pipeline + - title_md: rseqc + description_md: an RNA-seq quality control package + - title_md: salmon + description_md: Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq and single-cell data. + - title_md: sarscov2formatter + description_md: sarscov2formatter custom script + - title_md: sarscov2summary + description_md: sarscov2summary custom script + - title_md: scoary + description_md: Scoary calculates the assocations between all genes in the accessory + genome and the traits. + - title_md: semibin + description_md: 'SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural + Networks' + - title_md: seqkit + description_md: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation + - title_md: seqprep + description_md: Tool for merging paired-end Illumina reads and trimming adapters. + - title_md: seqsero2 + description_md: Salmonella serotype prediction from genome sequencing data + - title_md: shorah + description_md: Reconstruct haplotypes using ShoRAH in amplicon mode + - title_md: shovill + description_md: Faster de novo assembly pipeline based around Spades + - title_md: sistr_cmd + description_md: SISTR in silico serotyping tool + - title_md: smallgenomeutilities + description_md: Set of utilities for manipulating small viral genome data. + - title_md: smalt + description_md: SMALT aligns DNA sequencing reads with a reference genome. + - title_md: snap + description_md: SNAP is a general purpose gene finding program suitable for both + eukaryotic and prokaryotic genomes. + - title_md: snippy + description_md: Contains the snippy tool for characterising microbial snps + - title_md: sonneityping + description_md: Scripts for parsing Mykrobe predict results for Shigella sonnei. + - title_md: sortmerna + description_md: SortMeRNA is a software designed to rapidly filter ribosomal RNA + fragments from metatransriptomic data produced by next-generation sequencers. + - title_md: spades + description_md: '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.' + - title_md: spotyping + description_md: SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping + from sequence reads + - title_md: sr_bowtie + description_md: bowtie wrapper tool to align small RNA sequencing reads + - title_md: srst2 + description_md: Short Read Sequence Typing for Bacterial Pathogens + - title_md: srst2 + description_md: SRST2 Short Read Sequence Typing for Bacterial Pathogens + - title_md: staramr + description_md: Scan genome contigs against the ResFinder, PlasmidFinder, and + PointFinder antimicrobial resistance databases. + - title_md: stringmlst + description_md: Rapid and accurate identification of the sequence type (ST) + - title_md: structure + description_md: for using multi-locus genotype data to investigate population + structure. + - title_md: suite_qiime2__alignment + description_md: .nan + - title_md: suite_qiime2__composition + description_md: .nan + - title_md: suite_qiime2__cutadapt + description_md: .nan + - title_md: suite_qiime2__dada2 + description_md: .nan + - title_md: suite_qiime2__deblur + description_md: .nan + - title_md: suite_qiime2__demux + description_md: .nan + - title_md: suite_qiime2__diversity + description_md: .nan + - title_md: suite_qiime2__diversity_lib + description_md: .nan + - title_md: suite_qiime2__emperor + description_md: .nan + - title_md: suite_qiime2__feature_classifier + description_md: .nan + - title_md: suite_qiime2__feature_table + description_md: .nan + - title_md: suite_qiime2__fragment_insertion + description_md: .nan + - title_md: suite_qiime2__longitudinal + description_md: .nan + - title_md: suite_qiime2__metadata + description_md: .nan + - title_md: suite_qiime2__phylogeny + description_md: .nan + - title_md: suite_qiime2__quality_control + description_md: .nan + - title_md: suite_qiime2__quality_filter + description_md: .nan + - title_md: suite_qiime2__rescript + description_md: .nan + - title_md: suite_qiime2__sample_classifier + description_md: .nan + - title_md: suite_qiime2__taxa + description_md: .nan + - title_md: suite_qiime2__vsearch + description_md: .nan + - title_md: suite_qiime2_core + description_md: .nan + - title_md: suite_qiime2_core__tools + description_md: .nan + - title_md: t2ps + description_md: Draw phylogeny + - title_md: t2t_report + description_md: Summarize taxonomy + - title_md: t_coffee + description_md: T-Coffee + - title_md: taxonomy_krona_chart + description_md: Krona pie chart from taxonomic profile + - title_md: tb-profiler + description_md: Processes M. tuberculosis sequence data to infer strain type and + identify known drug resistance markers. + - title_md: tooldistillator + description_md: ToolDistillator extract and aggregate information from different + tool outputs to JSON parsable files + - title_md: transit + description_md: TRANSIT + - title_md: transtermhp + description_md: Finds rho-independent transcription terminators in bacterial genomes + - title_md: trim_galore + description_md: Trim Galore adaptive quality and adapter trimmer + - title_md: trycycler + description_md: Trycycler toolkit wrappers + - title_md: unicycler + description_md: Unicycler is a hybrid assembly pipeline for bacterial genomes. + - title_md: unipept + description_md: Unipept retrieves metaproteomics information + - title_md: uniprotxml_downloader + description_md: Download UniProt proteome in XML or fasta format + - title_md: usher + description_md: UShER toolkit wrappers + - title_md: valet + description_md: A pipeline for detecting mis-assemblies in metagenomic assemblies. + - title_md: vapor + description_md: Classify Influenza samples from raw short read sequence data + - title_md: varvamp + description_md: Variable VirusAMPlicons (varVAMP) is a tool to design primers + for highly diverse viruses + - title_md: vegan + description_md: an R package fo community ecologist + - title_md: velvet + description_md: de novo genomic assembler specially designed for short read sequencing + technologies + - title_md: velvet_optimiser + description_md: Automatically optimize Velvet assemblies + - title_md: virAnnot + description_md: virAnnot wrappers + - title_md: vsearch + description_md: VSEARCH including searching, clustering, chimera detection, dereplication, + sorting, masking and shuffling of sequences. + - title_md: wtdbg + description_md: WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads + assembly. diff --git a/sources/bin/populate_labs.py b/sources/bin/populate_labs.py index b08b7a8f..6e28ce12 100644 --- a/sources/bin/populate_labs.py +++ b/sources/bin/populate_labs.py @@ -45,10 +45,10 @@ def main() -> None: title_md = row[data.columns[0]] # Get the first column's value as title_md # Start the unordered list
    and construct each
  • for every other column in the row - description = "
      " - for column in data.columns[1:]: # Skip the first column (since it's title_md) - description += f"
    • {column}: {row[column]}
      • \n" - description += "
    " + description = row["Description"] + # for column in data.columns[1:]: # Skip the first column (since it's title_md) + # description += f"
  • {column}: {row[column]}
    • \n" + # description += "
" # Create the tool entry with the formatted HTML list tool_entry = { From 8ac12186f52c8c7b6083b6873322caa630309c1c Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 17:39:46 +0100 Subject: [PATCH 18/38] bla --- .../microgalaxy/lab/sections/5_tools.yml | 728 +----------------- 1 file changed, 1 insertion(+), 727 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 3318efec..af77fba6 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -15,730 +15,4 @@ tabs: - title_md: abritamr description_md: A pipeline for running AMRfinderPlus and collating results into functional classes - - title_md: abyss - description_md: Assembly By Short Sequences - a de novo, parallel, paired-end - sequence assembler - - title_md: aldex2 - description_md: Performs analysis Of differential abundance taking sample variation - into account - - title_md: amplican - description_md: AmpliCan is an analysis tool for genome editing. - - title_md: amrfinderplus - description_md: '"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.' - - title_md: ancombc - description_md: Performs analysis of compositions of microbiomes with bias correction. - - title_md: antismash - description_md: Antismash allows the genome-wide identification, annotation and - analysis of secondary metabolite biosynthesis gene clusters - - title_md: artic - description_md: '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' - - title_md: assemblystats - description_md: Summarise an assembly (e.g. N50 metrics) - - title_md: bakta - description_md: '"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."' - - title_md: bamtools - description_md: Operate on and transform BAM datasets in various ways using bamtools - - title_md: bandage - description_md: Bandage - A Bioinformatics Application for Navigating De novo - Assembly Graphs Easily - - title_md: bayescan - description_md: Detecting natural selection from population-based genetic data - - title_md: bbtools - description_md: 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. - - title_md: bigscape - description_md: Construct sequence similarity networks of BGCs and groups them - into GCF - - title_md: binning_refiner - description_md: Reconciles the outputs of different binning programs with the - aim to improve the quality of genome bins,especially with respect to contamination - levels. - - title_md: biohansel - description_md: Heidelberg and Enteritidis SNP Elucidation - - title_md: biom_format - description_md: The biom-format package provides a command line interface and - Python API for working with BIOM files. - - title_md: biotradis - description_md: Bio-Tradis is a tool suite dedicated to essentiality analyses - with TraDis data. - - title_md: blast2go - description_md: Maps BLAST results to GO annotation terms - - title_md: blast_rbh - description_md: BLAST Reciprocal Best Hits (RBH) from two FASTA files - - title_md: blastxml_to_top_descr - description_md: Make table of top BLAST match descriptions - - title_md: bracken - description_md: Bayesian Reestimation of Abundance with KrakEN - - title_md: busco - description_md: BUSCO assess genome and annotation completeness - - title_md: cat - description_md: Contig Annotation Tool (CAT) - - title_md: cd_hit_dup - description_md: simple tool for removing duplicates from sequencing reads - - title_md: cdhit - description_md: Cluster or compare biological sequence datasets - - title_md: cemitool - description_md: Gene co-expression network analysis tool - - title_md: checkm - description_md: Assess the quality of microbial genomes recovered from isolates, - single cells, and metagenomes - - title_md: clair3 - description_md: Symphonizing pileup and full-alignment for high-performance long-read - variant calling - - title_md: clinod - description_md: 'NoD: a Nucleolar localization sequence detector for eukaryotic - and viral proteins' - - title_md: clustalw - description_md: ClustalW multiple sequence alignment program for DNA or proteins - - title_md: cmsearch_deoverlap - description_md: removes lower scoring overlaps from cmsearch results. - - title_md: codeml - description_md: Detects positive selection - - title_md: cojac - description_md: co-occurrence of mutations on amplicons - - title_md: combine_assembly_stats - description_md: Combine multiple Assemblystats datasets into a single tabular - report - - title_md: combine_metaphlan_humann - description_md: Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species - abundances and gene families/pathways abundances - - title_md: compare_humann2_output - description_md: Compare outputs of HUMAnN2 for several samples and extract similar - and specific information - - title_md: compleasm - description_md: 'Compleasm: a faster and more accurate reimplementation of BUSCO' - - title_md: concoct - description_md: 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. - - title_md: coverm - description_md: CoverM genome and contig wrappers - - title_md: cryptogenotyper - description_md: CryptoGenotyper is a standalone tool to *in-silico* determine - species and subtype based on SSU rRNA and gp60 markers. - - title_md: cutadapt - description_md: Flexible tool to remove adapter sequences (and quality trim) high - throughput sequencing reads (fasta/fastq). - - title_md: dada2 - description_md: DADA2 wrappers - - title_md: das_tool - description_md: DAS Tool for genome resolved metagenomics - - title_md: deseq2 - description_md: Differential gene expression analysis based on the negative binomial - distribution - - title_md: diamond - description_md: DIAMOND is a new alignment tool for aligning short DNA sequencing - reads to a protein reference database such as NCBI-NR. - - title_md: disco - description_md: DISCO is a overlap-layout-consensus (OLC) metagenome assembler - - title_md: dram - description_md: DRAM for distilling microbial metabolism to automate the curation - of microbiome function - - title_md: drep - description_md: dRep compares and dereplicates genome sets - - title_md: ectyper - description_md: EC-Typer - in silico serotyping of Escherichia coli species - - title_md: effectiveT3 - description_md: Find bacterial type III effectors in protein sequences - - title_md: eggnog_mapper - description_md: eggnog-mapper fast functional annotation of novel sequences - - title_md: emboss_5 - description_md: Galaxy wrappers for EMBOSS version 5.0.0 tools - - title_md: ete - description_md: Analyse phylogenetic trees using the ETE Toolkit - - title_md: export2graphlan - description_md: export2graphlan is a conversion software tool for producing both - annotation and tree file for GraPhlAn - - title_md: ez_histograms - description_md: ggplot2 histograms and density plots - - title_md: fargene - description_md: fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) - - title_md: fastani - description_md: Fast alignment-free computation of whole-genome Average Nucleotide - Identity - - title_md: fastk - description_md: 'FastK: A K-mer counter (for HQ assembly data sets)' - - title_md: fastp - description_md: Fast all-in-one preprocessing for FASTQ files - - title_md: fastqe - description_md: FASTQE - - title_md: fasttree - description_md: FastTree infers approximately-maximum-likelihood phylogenetic - trees from alignments of nucleotide or protein sequences - GVL - - title_md: featurecounts - description_md: featureCounts counts the number of reads aligned to defined masked - regions in a reference genome - - title_md: filter_spades_repeats - description_md: Remove short and repeat contigs/scaffolds - - title_md: filtlong - description_md: Filtlong - Filtering long reads by quality - - title_md: flashlfq - description_md: FlashLFQ mass-spectrometry proteomics label-free quantification - - title_md: flye - description_md: Assembly of long and error-prone reads. - - title_md: format_metaphlan2_output - description_md: Format MetaPhlAn2 output to extract abundance at different taxonomic - levels - - title_md: fraggenescan - description_md: Tool for finding (fragmented) genes in short read - - title_md: freyja - description_md: lineage abundances estimation - - title_md: frogs - description_md: Suite for metabarcoding analysis - - title_md: funannotate - description_md: Funannotate is a genome prediction, annotation, and comparison - software package. - - title_md: getmlst - description_md: Download MLST datasets by species from pubmlst.org - - title_md: ggplot2 - description_md: 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. - - title_md: gi2taxonomy - description_md: Fetch taxonomic representation - - title_md: glimmer - description_md: Glimmer makes gene predictions. - - title_md: glimmer_hmm - description_md: GlimmerHMM is a new gene finder based on a Generalized Hidden - Markov Model (GHMM) - - title_md: goenrichment - description_md: Performs GO Enrichment analysis. - - title_md: goseq - description_md: goseq does selection-unbiased testing for category enrichment - amongst differentially expressed (DE) genes for RNA-seq data - - title_md: graphlan - description_md: GraPhlAn is a software tool for producing high-quality circular - representations of taxonomic and phylogenetic trees - - title_md: graphmap - description_md: Mapper for long, error-prone reads. - - title_md: gtdbtk - description_md: '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. ' - - title_md: gubbins - description_md: Gubbins - bacterial recombination detection - - title_md: hamronization - description_md: Convert AMR gene detection tool output to hAMRonization specification - format. - - title_md: hansel - description_md: Heidelberg and Enteritidis SNP Elucidation - - title_md: hifiasm_meta - description_md: A hifiasm fork for metagenome assembly using Hifi reads. - - title_md: hivtrace - description_md: 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. - - title_md: hmmer3 - description_md: 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). - - title_md: humann - description_md: HUMAnN for functionally profiling metagenomes and metatranscriptomes - at species-level resolution - - title_md: hyphy - description_md: Hypothesis Testing using Phylogenies - - title_md: hypo - description_md: Super Fast & Accurate Polisher for Long Read Genome Assemblies - - title_md: icescreen - description_md: ICEscreen identifies Integrative Conjugative Elements (ICEs) and - Integrative Mobilizable Elements (IMEs) in Bacillota genomes. - - title_md: idba_ud - description_md: Wrappers for the idba assembler variants. - - title_md: infernal - description_md: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence - databases for RNA structure and sequence similarities. - - title_md: instrain - description_md: InStrain is a tool for analysis of co-occurring genome populations - from metagenomes - - title_md: integron_finder - description_md: '"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"' - - title_md: interproscan - description_md: Interproscan queries the interpro database and provides annotations. - - title_md: iprscan5 - description_md: Interproscan queries the interpro database and provides annotations. - - title_md: iqtree - description_md: Efficient phylogenomic software by maximum likelihood - - title_md: isescan - description_md: '"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."' - - title_md: itsx - description_md: ITSx is an open source software utility to extract the highly - variable ITS1 and ITS2 subregions from ITS sequences. - - title_md: ivar - description_md: iVar is a computational package that contains functions broadly - useful for viral amplicon-based sequencing - - title_md: jbrowse - description_md: JBrowse Genome Browser integrated as a Galaxy Tool - - title_md: jellyfish - description_md: Jellyfish is a tool for fast, memory-efficient counting of k-mers - in DNA - - title_md: kat_filter - description_md: Filtering kmers or reads from a database of kmers hashes - - title_md: kc-align - description_md: Kc-Align custom tool - - title_md: khmer - description_md: In-memory nucleotide sequence k-mer counting, filtering, graph - traversal and more - - title_md: kleborate - description_md: Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella - pneumoniae species complex (KpSC) - - title_md: kofamscan - description_md: Gene function annotation tool based on KEGG Orthology and hidden - Markov model - - title_md: kraken - description_md: 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. - - title_md: kraken2 - description_md: Kraken2 for taxonomic designation. - - title_md: kraken2tax - description_md: Convert Kraken output to Galaxy taxonomy data. - - title_md: kraken_biom - description_md: Create BIOM-format tables (http://biom-format.org) from Kraken - output (http://ccb.jhu.edu/software/kraken/) - - title_md: kraken_taxonomy_report - description_md: Kraken taxonomy report - - title_md: krakentools - description_md: KrakenTools is a suite of scripts to be used alongside the Kraken - - title_md: krocus - description_md: Predict MLST directly from uncorrected long reads - - title_md: lca_wrapper - description_md: Find lowest diagnostic rank - - title_md: legsta - description_md: Performs in silico Legionella pneumophila sequence based typing. - - title_md: lighter - description_md: Lighter is a kmer-based error correction method for whole genome - sequencing data - - title_md: limma_voom - description_md: Perform RNA-Seq differential expression analysis using limma voom - pipeline - - title_md: lineagespot - description_md: Identification of SARS-CoV-2 related metagenomic mutations based - on a single (or a list of) variant(s) file(s) - - title_md: lorikeet - description_md: Tools for M. tuberculosis DNA fingerprinting (spoligotyping) - - title_md: lotus2 - description_md: LotuS2 OTU processing pipeline - - title_md: m6anet - description_md: m6anet to detect m6A RNA modifications from nanopore data - - title_md: maaslin2 - description_md: MaAsLin2 is comprehensive R package for efficiently determining - multivariable association between microbial meta'omic features and clinical - metadata. - - title_md: mafft - description_md: Multiple alignment program for amino acid or nucleotide sequences - - title_md: make_nr - description_md: Make a FASTA file non-redundant - - title_md: maker - description_md: 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. - - title_md: mapseq - description_md: fast and accurate sequence read classification tool designed to - assign taxonomy and OTU classifications to ribosomal RNA sequences. - - title_md: mash - description_md: Fast genome and metagenome distance estimation using MinHash - - title_md: maxbin2 - description_md: clusters metagenomic contigs into bins - - title_md: maxquant - description_md: wrapper for MaxQuant - - title_md: mcl - description_md: The Markov Cluster Algorithm, a cluster algorithm for graphs - - title_md: medaka - description_md: Sequence correction provided by ONT Research - - title_md: megahit - description_md: An ultra-fast single-node solution for large and complex metagenomics - assembly via succinct de Bruijn graph. - - title_md: megahit_contig2fastg - description_md: A subprogram within the Megahit toolkit for converting contigs - to assembly graphs (fastg) - - title_md: megan - description_md: 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). - - title_md: meningotype - description_md: Assign sequence type to N. meningitidis genome assemblies - - title_md: merqury - description_md: Merqury is a tool for evaluating genomes assemblies based of k-mer - operations. - - title_md: meryl - description_md: Meryl a k-mer counter. - - title_md: metabat2 - description_md: 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. - - title_md: metaeuk - description_md: '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. ' - - title_md: metagene_annotator - description_md: MetaGeneAnnotator gene-finding program for prokaryote and phage - - title_md: metagenomeseq - description_md: metagenomeSeq Normalization - - title_md: metanovo - description_md: Produce targeted databases for mass spectrometry analysis. - - title_md: metaphlan - description_md: MetaPhlAn for Metagenomic Phylogenetic Analysis - - title_md: metaquantome - description_md: quantitative analysis of microbiome taxonomy and function - - title_md: metawrapmg - description_md: A flexible pipeline for genome-resolved metagenomic data analysis - - title_md: minia - description_md: Short-read assembler based on a de Bruijn graph - - title_md: miniasm - description_md: Miniasm - Ultrafast de novo assembly for long noisy reads (though - having no consensus step) - - title_md: minipolish - description_md: Polishing miniasm assemblies - - title_md: miniprot - description_md: Align a protein sequence against a genome with affine gap penalty, - splicing and frameshift. - - title_md: mitos - description_md: de-novo annotation of metazoan mitochondrial genomes - - title_md: mlst - description_md: Scan contig files against PubMLST typing schemes - - title_md: mob_suite - description_md: MOB-suite is a set of software tools for clustering, reconstruction - and typing of plasmids from draft assemblies - - title_md: mothur - description_md: Mothur wrappers - - title_md: mrbayes - description_md: A program for the Bayesian estimation of phylogeny. - - title_md: msconvert - description_md: msconvert Convert and/or filter mass spectrometry files (including - vendor formats) using the official Docker container - - title_md: msstatstmt - description_md: MSstatsTMT protein significance analysis in shotgun mass spectrometry-based - proteomic experiments with tandem mass tag (TMT) labeling - - title_md: multigsea - description_md: GSEA-based pathway enrichment analysis for multi-omics data - - title_md: multiqc - description_md: MultiQC aggregates results from bioinformatics analyses across - many samples into a single report - - title_md: mykrobe - description_md: Antibiotic resistance predictions - - title_md: mykrobe_parser - description_md: RScript to parse the results of mykrobe predictor. - - title_md: mz_to_sqlite - description_md: Creates a SQLite database for proteomics data - - title_md: nanocompore - description_md: 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. - - title_md: nanoplot - description_md: Plotting tool for long read sequencing data and alignments - - title_md: nanopolishcomp - description_md: 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. - - title_md: ncbi_blast_plus - description_md: NCBI BLAST+ - - title_md: ncbi_fcs_gx - description_md: FCS-GX detects contamination from foreign organisms in genome - sequences using the genome cross-species aligner (GX). - - title_md: newick_utils - description_md: Perform operations on Newick trees - - title_md: nextclade - description_md: Identify differences between your sequences and a reference sequence - used by Nextstrain - - title_md: nextdenovo - description_md: String graph-based de novo assembler for long reads - - title_md: nonpareil - description_md: Estimate average coverage in metagenomic datasets - - title_md: nucleosome_prediction - description_md: Prediction of Nucleosomes Positions on the Genome - - title_md: nugen_nudup - description_md: Marks/removes PCR introduced duplicate molecules based on the - molecular tagging technology used in NuGEN products. - - title_md: obisindicators - description_md: Compute biodiveristy indicators for marine data from obis - - title_md: obitools - description_md: OBITools is a set of programs developed to simplify the manipulation - of sequence files - - title_md: omark - description_md: Proteome quality assessment software - - title_md: orfipy - description_md: Galaxy wrapper for ORFIPY - - title_md: orthofinder - description_md: Accurate inference of orthologous gene groups made easy - - title_md: peptideshaker - description_md: PeptideShaker and SearchGUI - - title_md: pfamscan - description_md: Search a FASTA sequence against a library of Pfam HMM. - - title_md: pharokka - description_md: rapid standardised annotation tool for bacteriophage genomes and - metagenomes - - title_md: phyloseq - description_md: Handling and analysis of high-throughput microbiome census data - - title_md: phyml - description_md: PhyML is a phylogeny software based on the maximum-likelihood - principle. - - title_md: picrust - description_md: PICRUSt wrappers - - title_md: picrust2 - description_md: 'PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction - of Unobserved States' - - title_md: plasflow - description_md: PlasFlow - Prediction of plasmid sequences in metagenomic contigs. - - title_md: plasmidfinder - description_md: '"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"' - - title_md: plasmidspades - description_md: Genome assembler for assemblying plasmid - - title_md: polypolish - description_md: '"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."' - - title_md: prodigal - description_md: A protein-coding gene prediction software tool for bacterial and - archaeal genomes - - title_md: prokka - description_md: Rapid annotation of prokaryotic genomes - - title_md: promer - description_md: Aligns two sets of contigs and reports amino acid substitutions - between them - - title_md: proteinortho - description_md: Proteinortho is a tool to detect orthologous proteins/genes within - different species. - - title_md: pycoqc - description_md: QC metrics for ONT Basecalling - - title_md: pygenometracks - description_md: 'pyGenomeTracks: Standalone program and library to plot beautiful - genome browser tracks.' - - title_md: qiime_add_on - description_md: QIIME to perform microbial community analysis - - title_md: qiime_core - description_md: QIIME to perform microbial community analysis - - title_md: qualimap - description_md: 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. - - title_md: quast - description_md: Quast (Quality ASsessment Tool) evaluates genome assemblies. - - title_md: quickmerge - description_md: Merge long-read and hybrid assemblies to increase contiguity - - title_md: rRNA - description_md: Identification of ribosomal RNA genes in metagenomic fragments. - - title_md: racon - description_md: Consensus module for raw de novo DNA assembly of long uncorrected - reads. - - title_md: rasusa - description_md: Randomly subsample sequencing reads to a specified coverage - - title_md: raxml - description_md: RAxML - A Maximum Likelihood based phylogenetic inference - - title_md: read_it_and_keep - description_md: Rapid decontamination of SARS-CoV-2 sequencing reads - - title_md: reago - description_md: Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic - data. - - title_md: recentrifuge - description_md: '"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."' - - title_md: repeatexplorer2 - description_md: Tool for annotation of repeats from unassembled shotgun reads. - - title_md: roary - description_md: Roary the pangenome pipeline - - title_md: rseqc - description_md: an RNA-seq quality control package - - title_md: salmon - description_md: Salmon is a wicked-fast program to produce a highly-accurate, - transcript-level quantification estimates from RNA-seq and single-cell data. - - title_md: sarscov2formatter - description_md: sarscov2formatter custom script - - title_md: sarscov2summary - description_md: sarscov2summary custom script - - title_md: scoary - description_md: Scoary calculates the assocations between all genes in the accessory - genome and the traits. - - title_md: semibin - description_md: 'SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural - Networks' - - title_md: seqkit - description_md: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation - - title_md: seqprep - description_md: Tool for merging paired-end Illumina reads and trimming adapters. - - title_md: seqsero2 - description_md: Salmonella serotype prediction from genome sequencing data - - title_md: shorah - description_md: Reconstruct haplotypes using ShoRAH in amplicon mode - - title_md: shovill - description_md: Faster de novo assembly pipeline based around Spades - - title_md: sistr_cmd - description_md: SISTR in silico serotyping tool - - title_md: smallgenomeutilities - description_md: Set of utilities for manipulating small viral genome data. - - title_md: smalt - description_md: SMALT aligns DNA sequencing reads with a reference genome. - - title_md: snap - description_md: SNAP is a general purpose gene finding program suitable for both - eukaryotic and prokaryotic genomes. - - title_md: snippy - description_md: Contains the snippy tool for characterising microbial snps - - title_md: sonneityping - description_md: Scripts for parsing Mykrobe predict results for Shigella sonnei. - - title_md: sortmerna - description_md: SortMeRNA is a software designed to rapidly filter ribosomal RNA - fragments from metatransriptomic data produced by next-generation sequencers. - - title_md: spades - description_md: '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.' - - title_md: spotyping - description_md: SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping - from sequence reads - - title_md: sr_bowtie - description_md: bowtie wrapper tool to align small RNA sequencing reads - - title_md: srst2 - description_md: Short Read Sequence Typing for Bacterial Pathogens - - title_md: srst2 - description_md: SRST2 Short Read Sequence Typing for Bacterial Pathogens - - title_md: staramr - description_md: Scan genome contigs against the ResFinder, PlasmidFinder, and - PointFinder antimicrobial resistance databases. - - title_md: stringmlst - description_md: Rapid and accurate identification of the sequence type (ST) - - title_md: structure - description_md: for using multi-locus genotype data to investigate population - structure. - - title_md: suite_qiime2__alignment - description_md: .nan - - title_md: suite_qiime2__composition - description_md: .nan - - title_md: suite_qiime2__cutadapt - description_md: .nan - - title_md: suite_qiime2__dada2 - description_md: .nan - - title_md: suite_qiime2__deblur - description_md: .nan - - title_md: suite_qiime2__demux - description_md: .nan - - title_md: suite_qiime2__diversity - description_md: .nan - - title_md: suite_qiime2__diversity_lib - description_md: .nan - - title_md: suite_qiime2__emperor - description_md: .nan - - title_md: suite_qiime2__feature_classifier - description_md: .nan - - title_md: suite_qiime2__feature_table - description_md: .nan - - title_md: suite_qiime2__fragment_insertion - description_md: .nan - - title_md: suite_qiime2__longitudinal - description_md: .nan - - title_md: suite_qiime2__metadata - description_md: .nan - - title_md: suite_qiime2__phylogeny - description_md: .nan - - title_md: suite_qiime2__quality_control - description_md: .nan - - title_md: suite_qiime2__quality_filter - description_md: .nan - - title_md: suite_qiime2__rescript - description_md: .nan - - title_md: suite_qiime2__sample_classifier - description_md: .nan - - title_md: suite_qiime2__taxa - description_md: .nan - - title_md: suite_qiime2__vsearch - description_md: .nan - - title_md: suite_qiime2_core - description_md: .nan - - title_md: suite_qiime2_core__tools - description_md: .nan - - title_md: t2ps - description_md: Draw phylogeny - - title_md: t2t_report - description_md: Summarize taxonomy - - title_md: t_coffee - description_md: T-Coffee - - title_md: taxonomy_krona_chart - description_md: Krona pie chart from taxonomic profile - - title_md: tb-profiler - description_md: Processes M. tuberculosis sequence data to infer strain type and - identify known drug resistance markers. - - title_md: tooldistillator - description_md: ToolDistillator extract and aggregate information from different - tool outputs to JSON parsable files - - title_md: transit - description_md: TRANSIT - - title_md: transtermhp - description_md: Finds rho-independent transcription terminators in bacterial genomes - - title_md: trim_galore - description_md: Trim Galore adaptive quality and adapter trimmer - - title_md: trycycler - description_md: Trycycler toolkit wrappers - - title_md: unicycler - description_md: Unicycler is a hybrid assembly pipeline for bacterial genomes. - - title_md: unipept - description_md: Unipept retrieves metaproteomics information - - title_md: uniprotxml_downloader - description_md: Download UniProt proteome in XML or fasta format - - title_md: usher - description_md: UShER toolkit wrappers - - title_md: valet - description_md: A pipeline for detecting mis-assemblies in metagenomic assemblies. - - title_md: vapor - description_md: Classify Influenza samples from raw short read sequence data - - title_md: varvamp - description_md: Variable VirusAMPlicons (varVAMP) is a tool to design primers - for highly diverse viruses - - title_md: vegan - description_md: an R package fo community ecologist - - title_md: velvet - description_md: de novo genomic assembler specially designed for short read sequencing - technologies - - title_md: velvet_optimiser - description_md: Automatically optimize Velvet assemblies - - title_md: virAnnot - description_md: virAnnot wrappers - - title_md: vsearch - description_md: VSEARCH including searching, clustering, chimera detection, dereplication, - sorting, masking and shuffling of sequences. - - title_md: wtdbg - description_md: WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads - assembly. + \ No newline at end of file From d336c204572faaf2b4974f3ef31a9cb1ded61f78 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 17:40:58 +0100 Subject: [PATCH 19/38] bla --- .../microgalaxy/lab/sections/5_tools.yml | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index af77fba6..f86b3579 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -1,18 +1,18 @@ id: tools title: Community Tools tabs: -- id: tool_list - title: List of community curated tools available for microGalaxy - content: - - title_md: PAMPA - description_md: Tools to compute and analyse biodiversity metrics - - title_md: TreeBest - description_md: TreeBeST best - - title_md: abacas - description_md: Order and Orientate Contigs - - title_md: abricate - description_md: Mass screening of contigs for antiobiotic resistance genes - - title_md: abritamr - description_md: A pipeline for running AMRfinderPlus and collating results into - functional classes - \ No newline at end of file + - id: tool_list + title: List of community curated tools available for microGalaxy + content: + - title_md: PAMPA + description_md: Tools to compute and analyse biodiversity metrics + - title_md: TreeBest + description_md: TreeBeST best + - title_md: abacas + description_md: Order and Orientate Contigs + - title_md: abricate + description_md: Mass screening of contigs for antiobiotic resistance genes + - title_md: abritamr + description_md: A pipeline for running AMRfinderPlus and collating results into + functional classes + \ No newline at end of file From 698bdd1998d5ef743342512936de060d55d7faae Mon Sep 17 00:00:00 2001 From: paulzierep Date: Fri, 8 Nov 2024 10:08:36 +0100 Subject: [PATCH 20/38] All tools --- .../microgalaxy/lab/sections/5_tools.yml | 756 +++++++++++++++++- 1 file changed, 741 insertions(+), 15 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index f86b3579..3318efec 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -1,18 +1,744 @@ id: tools title: Community Tools tabs: - - id: tool_list - title: List of community curated tools available for microGalaxy - content: - - title_md: PAMPA - description_md: Tools to compute and analyse biodiversity metrics - - title_md: TreeBest - description_md: TreeBeST best - - title_md: abacas - description_md: Order and Orientate Contigs - - title_md: abricate - description_md: Mass screening of contigs for antiobiotic resistance genes - - title_md: abritamr - description_md: A pipeline for running AMRfinderPlus and collating results into - functional classes - \ No newline at end of file +- id: tool_list + title: List of community curated tools available for microGalaxy + content: + - title_md: PAMPA + description_md: Tools to compute and analyse biodiversity metrics + - title_md: TreeBest + description_md: TreeBeST best + - title_md: abacas + description_md: Order and Orientate Contigs + - title_md: abricate + description_md: Mass screening of contigs for antiobiotic resistance genes + - title_md: abritamr + description_md: A pipeline for running AMRfinderPlus and collating results into + functional classes + - title_md: abyss + description_md: Assembly By Short Sequences - a de novo, parallel, paired-end + sequence assembler + - title_md: aldex2 + description_md: Performs analysis Of differential abundance taking sample variation + into account + - title_md: amplican + description_md: AmpliCan is an analysis tool for genome editing. + - title_md: amrfinderplus + description_md: '"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.' + - title_md: ancombc + description_md: Performs analysis of compositions of microbiomes with bias correction. + - title_md: antismash + description_md: Antismash allows the genome-wide identification, annotation and + analysis of secondary metabolite biosynthesis gene clusters + - title_md: artic + description_md: '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' + - title_md: assemblystats + description_md: Summarise an assembly (e.g. N50 metrics) + - title_md: bakta + description_md: '"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."' + - title_md: bamtools + description_md: Operate on and transform BAM datasets in various ways using bamtools + - title_md: bandage + description_md: Bandage - A Bioinformatics Application for Navigating De novo + Assembly Graphs Easily + - title_md: bayescan + description_md: Detecting natural selection from population-based genetic data + - title_md: bbtools + description_md: 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. + - title_md: bigscape + description_md: Construct sequence similarity networks of BGCs and groups them + into GCF + - title_md: binning_refiner + description_md: Reconciles the outputs of different binning programs with the + aim to improve the quality of genome bins,especially with respect to contamination + levels. + - title_md: biohansel + description_md: Heidelberg and Enteritidis SNP Elucidation + - title_md: biom_format + description_md: The biom-format package provides a command line interface and + Python API for working with BIOM files. + - title_md: biotradis + description_md: Bio-Tradis is a tool suite dedicated to essentiality analyses + with TraDis data. + - title_md: blast2go + description_md: Maps BLAST results to GO annotation terms + - title_md: blast_rbh + description_md: BLAST Reciprocal Best Hits (RBH) from two FASTA files + - title_md: blastxml_to_top_descr + description_md: Make table of top BLAST match descriptions + - title_md: bracken + description_md: Bayesian Reestimation of Abundance with KrakEN + - title_md: busco + description_md: BUSCO assess genome and annotation completeness + - title_md: cat + description_md: Contig Annotation Tool (CAT) + - title_md: cd_hit_dup + description_md: simple tool for removing duplicates from sequencing reads + - title_md: cdhit + description_md: Cluster or compare biological sequence datasets + - title_md: cemitool + description_md: Gene co-expression network analysis tool + - title_md: checkm + description_md: Assess the quality of microbial genomes recovered from isolates, + single cells, and metagenomes + - title_md: clair3 + description_md: Symphonizing pileup and full-alignment for high-performance long-read + variant calling + - title_md: clinod + description_md: 'NoD: a Nucleolar localization sequence detector for eukaryotic + and viral proteins' + - title_md: clustalw + description_md: ClustalW multiple sequence alignment program for DNA or proteins + - title_md: cmsearch_deoverlap + description_md: removes lower scoring overlaps from cmsearch results. + - title_md: codeml + description_md: Detects positive selection + - title_md: cojac + description_md: co-occurrence of mutations on amplicons + - title_md: combine_assembly_stats + description_md: Combine multiple Assemblystats datasets into a single tabular + report + - title_md: combine_metaphlan_humann + description_md: Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species + abundances and gene families/pathways abundances + - title_md: compare_humann2_output + description_md: Compare outputs of HUMAnN2 for several samples and extract similar + and specific information + - title_md: compleasm + description_md: 'Compleasm: a faster and more accurate reimplementation of BUSCO' + - title_md: concoct + description_md: 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. + - title_md: coverm + description_md: CoverM genome and contig wrappers + - title_md: cryptogenotyper + description_md: CryptoGenotyper is a standalone tool to *in-silico* determine + species and subtype based on SSU rRNA and gp60 markers. + - title_md: cutadapt + description_md: Flexible tool to remove adapter sequences (and quality trim) high + throughput sequencing reads (fasta/fastq). + - title_md: dada2 + description_md: DADA2 wrappers + - title_md: das_tool + description_md: DAS Tool for genome resolved metagenomics + - title_md: deseq2 + description_md: Differential gene expression analysis based on the negative binomial + distribution + - title_md: diamond + description_md: DIAMOND is a new alignment tool for aligning short DNA sequencing + reads to a protein reference database such as NCBI-NR. + - title_md: disco + description_md: DISCO is a overlap-layout-consensus (OLC) metagenome assembler + - title_md: dram + description_md: DRAM for distilling microbial metabolism to automate the curation + of microbiome function + - title_md: drep + description_md: dRep compares and dereplicates genome sets + - title_md: ectyper + description_md: EC-Typer - in silico serotyping of Escherichia coli species + - title_md: effectiveT3 + description_md: Find bacterial type III effectors in protein sequences + - title_md: eggnog_mapper + description_md: eggnog-mapper fast functional annotation of novel sequences + - title_md: emboss_5 + description_md: Galaxy wrappers for EMBOSS version 5.0.0 tools + - title_md: ete + description_md: Analyse phylogenetic trees using the ETE Toolkit + - title_md: export2graphlan + description_md: export2graphlan is a conversion software tool for producing both + annotation and tree file for GraPhlAn + - title_md: ez_histograms + description_md: ggplot2 histograms and density plots + - title_md: fargene + description_md: fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) + - title_md: fastani + description_md: Fast alignment-free computation of whole-genome Average Nucleotide + Identity + - title_md: fastk + description_md: 'FastK: A K-mer counter (for HQ assembly data sets)' + - title_md: fastp + description_md: Fast all-in-one preprocessing for FASTQ files + - title_md: fastqe + description_md: FASTQE + - title_md: fasttree + description_md: FastTree infers approximately-maximum-likelihood phylogenetic + trees from alignments of nucleotide or protein sequences - GVL + - title_md: featurecounts + description_md: featureCounts counts the number of reads aligned to defined masked + regions in a reference genome + - title_md: filter_spades_repeats + description_md: Remove short and repeat contigs/scaffolds + - title_md: filtlong + description_md: Filtlong - Filtering long reads by quality + - title_md: flashlfq + description_md: FlashLFQ mass-spectrometry proteomics label-free quantification + - title_md: flye + description_md: Assembly of long and error-prone reads. + - title_md: format_metaphlan2_output + description_md: Format MetaPhlAn2 output to extract abundance at different taxonomic + levels + - title_md: fraggenescan + description_md: Tool for finding (fragmented) genes in short read + - title_md: freyja + description_md: lineage abundances estimation + - title_md: frogs + description_md: Suite for metabarcoding analysis + - title_md: funannotate + description_md: Funannotate is a genome prediction, annotation, and comparison + software package. + - title_md: getmlst + description_md: Download MLST datasets by species from pubmlst.org + - title_md: ggplot2 + description_md: 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. + - title_md: gi2taxonomy + description_md: Fetch taxonomic representation + - title_md: glimmer + description_md: Glimmer makes gene predictions. + - title_md: glimmer_hmm + description_md: GlimmerHMM is a new gene finder based on a Generalized Hidden + Markov Model (GHMM) + - title_md: goenrichment + description_md: Performs GO Enrichment analysis. + - title_md: goseq + description_md: goseq does selection-unbiased testing for category enrichment + amongst differentially expressed (DE) genes for RNA-seq data + - title_md: graphlan + description_md: GraPhlAn is a software tool for producing high-quality circular + representations of taxonomic and phylogenetic trees + - title_md: graphmap + description_md: Mapper for long, error-prone reads. + - title_md: gtdbtk + description_md: '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. ' + - title_md: gubbins + description_md: Gubbins - bacterial recombination detection + - title_md: hamronization + description_md: Convert AMR gene detection tool output to hAMRonization specification + format. + - title_md: hansel + description_md: Heidelberg and Enteritidis SNP Elucidation + - title_md: hifiasm_meta + description_md: A hifiasm fork for metagenome assembly using Hifi reads. + - title_md: hivtrace + description_md: 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. + - title_md: hmmer3 + description_md: 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). + - title_md: humann + description_md: HUMAnN for functionally profiling metagenomes and metatranscriptomes + at species-level resolution + - title_md: hyphy + description_md: Hypothesis Testing using Phylogenies + - title_md: hypo + description_md: Super Fast & Accurate Polisher for Long Read Genome Assemblies + - title_md: icescreen + description_md: ICEscreen identifies Integrative Conjugative Elements (ICEs) and + Integrative Mobilizable Elements (IMEs) in Bacillota genomes. + - title_md: idba_ud + description_md: Wrappers for the idba assembler variants. + - title_md: infernal + description_md: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence + databases for RNA structure and sequence similarities. + - title_md: instrain + description_md: InStrain is a tool for analysis of co-occurring genome populations + from metagenomes + - title_md: integron_finder + description_md: '"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"' + - title_md: interproscan + description_md: Interproscan queries the interpro database and provides annotations. + - title_md: iprscan5 + description_md: Interproscan queries the interpro database and provides annotations. + - title_md: iqtree + description_md: Efficient phylogenomic software by maximum likelihood + - title_md: isescan + description_md: '"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."' + - title_md: itsx + description_md: ITSx is an open source software utility to extract the highly + variable ITS1 and ITS2 subregions from ITS sequences. + - title_md: ivar + description_md: iVar is a computational package that contains functions broadly + useful for viral amplicon-based sequencing + - title_md: jbrowse + description_md: JBrowse Genome Browser integrated as a Galaxy Tool + - title_md: jellyfish + description_md: Jellyfish is a tool for fast, memory-efficient counting of k-mers + in DNA + - title_md: kat_filter + description_md: Filtering kmers or reads from a database of kmers hashes + - title_md: kc-align + description_md: Kc-Align custom tool + - title_md: khmer + description_md: In-memory nucleotide sequence k-mer counting, filtering, graph + traversal and more + - title_md: kleborate + description_md: Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella + pneumoniae species complex (KpSC) + - title_md: kofamscan + description_md: Gene function annotation tool based on KEGG Orthology and hidden + Markov model + - title_md: kraken + description_md: 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. + - title_md: kraken2 + description_md: Kraken2 for taxonomic designation. + - title_md: kraken2tax + description_md: Convert Kraken output to Galaxy taxonomy data. + - title_md: kraken_biom + description_md: Create BIOM-format tables (http://biom-format.org) from Kraken + output (http://ccb.jhu.edu/software/kraken/) + - title_md: kraken_taxonomy_report + description_md: Kraken taxonomy report + - title_md: krakentools + description_md: KrakenTools is a suite of scripts to be used alongside the Kraken + - title_md: krocus + description_md: Predict MLST directly from uncorrected long reads + - title_md: lca_wrapper + description_md: Find lowest diagnostic rank + - title_md: legsta + description_md: Performs in silico Legionella pneumophila sequence based typing. + - title_md: lighter + description_md: Lighter is a kmer-based error correction method for whole genome + sequencing data + - title_md: limma_voom + description_md: Perform RNA-Seq differential expression analysis using limma voom + pipeline + - title_md: lineagespot + description_md: Identification of SARS-CoV-2 related metagenomic mutations based + on a single (or a list of) variant(s) file(s) + - title_md: lorikeet + description_md: Tools for M. tuberculosis DNA fingerprinting (spoligotyping) + - title_md: lotus2 + description_md: LotuS2 OTU processing pipeline + - title_md: m6anet + description_md: m6anet to detect m6A RNA modifications from nanopore data + - title_md: maaslin2 + description_md: MaAsLin2 is comprehensive R package for efficiently determining + multivariable association between microbial meta'omic features and clinical + metadata. + - title_md: mafft + description_md: Multiple alignment program for amino acid or nucleotide sequences + - title_md: make_nr + description_md: Make a FASTA file non-redundant + - title_md: maker + description_md: 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. + - title_md: mapseq + description_md: fast and accurate sequence read classification tool designed to + assign taxonomy and OTU classifications to ribosomal RNA sequences. + - title_md: mash + description_md: Fast genome and metagenome distance estimation using MinHash + - title_md: maxbin2 + description_md: clusters metagenomic contigs into bins + - title_md: maxquant + description_md: wrapper for MaxQuant + - title_md: mcl + description_md: The Markov Cluster Algorithm, a cluster algorithm for graphs + - title_md: medaka + description_md: Sequence correction provided by ONT Research + - title_md: megahit + description_md: An ultra-fast single-node solution for large and complex metagenomics + assembly via succinct de Bruijn graph. + - title_md: megahit_contig2fastg + description_md: A subprogram within the Megahit toolkit for converting contigs + to assembly graphs (fastg) + - title_md: megan + description_md: 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). + - title_md: meningotype + description_md: Assign sequence type to N. meningitidis genome assemblies + - title_md: merqury + description_md: Merqury is a tool for evaluating genomes assemblies based of k-mer + operations. + - title_md: meryl + description_md: Meryl a k-mer counter. + - title_md: metabat2 + description_md: 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. + - title_md: metaeuk + description_md: '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. ' + - title_md: metagene_annotator + description_md: MetaGeneAnnotator gene-finding program for prokaryote and phage + - title_md: metagenomeseq + description_md: metagenomeSeq Normalization + - title_md: metanovo + description_md: Produce targeted databases for mass spectrometry analysis. + - title_md: metaphlan + description_md: MetaPhlAn for Metagenomic Phylogenetic Analysis + - title_md: metaquantome + description_md: quantitative analysis of microbiome taxonomy and function + - title_md: metawrapmg + description_md: A flexible pipeline for genome-resolved metagenomic data analysis + - title_md: minia + description_md: Short-read assembler based on a de Bruijn graph + - title_md: miniasm + description_md: Miniasm - Ultrafast de novo assembly for long noisy reads (though + having no consensus step) + - title_md: minipolish + description_md: Polishing miniasm assemblies + - title_md: miniprot + description_md: Align a protein sequence against a genome with affine gap penalty, + splicing and frameshift. + - title_md: mitos + description_md: de-novo annotation of metazoan mitochondrial genomes + - title_md: mlst + description_md: Scan contig files against PubMLST typing schemes + - title_md: mob_suite + description_md: MOB-suite is a set of software tools for clustering, reconstruction + and typing of plasmids from draft assemblies + - title_md: mothur + description_md: Mothur wrappers + - title_md: mrbayes + description_md: A program for the Bayesian estimation of phylogeny. + - title_md: msconvert + description_md: msconvert Convert and/or filter mass spectrometry files (including + vendor formats) using the official Docker container + - title_md: msstatstmt + description_md: MSstatsTMT protein significance analysis in shotgun mass spectrometry-based + proteomic experiments with tandem mass tag (TMT) labeling + - title_md: multigsea + description_md: GSEA-based pathway enrichment analysis for multi-omics data + - title_md: multiqc + description_md: MultiQC aggregates results from bioinformatics analyses across + many samples into a single report + - title_md: mykrobe + description_md: Antibiotic resistance predictions + - title_md: mykrobe_parser + description_md: RScript to parse the results of mykrobe predictor. + - title_md: mz_to_sqlite + description_md: Creates a SQLite database for proteomics data + - title_md: nanocompore + description_md: 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. + - title_md: nanoplot + description_md: Plotting tool for long read sequencing data and alignments + - title_md: nanopolishcomp + description_md: 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. + - title_md: ncbi_blast_plus + description_md: NCBI BLAST+ + - title_md: ncbi_fcs_gx + description_md: FCS-GX detects contamination from foreign organisms in genome + sequences using the genome cross-species aligner (GX). + - title_md: newick_utils + description_md: Perform operations on Newick trees + - title_md: nextclade + description_md: Identify differences between your sequences and a reference sequence + used by Nextstrain + - title_md: nextdenovo + description_md: String graph-based de novo assembler for long reads + - title_md: nonpareil + description_md: Estimate average coverage in metagenomic datasets + - title_md: nucleosome_prediction + description_md: Prediction of Nucleosomes Positions on the Genome + - title_md: nugen_nudup + description_md: Marks/removes PCR introduced duplicate molecules based on the + molecular tagging technology used in NuGEN products. + - title_md: obisindicators + description_md: Compute biodiveristy indicators for marine data from obis + - title_md: obitools + description_md: OBITools is a set of programs developed to simplify the manipulation + of sequence files + - title_md: omark + description_md: Proteome quality assessment software + - title_md: orfipy + description_md: Galaxy wrapper for ORFIPY + - title_md: orthofinder + description_md: Accurate inference of orthologous gene groups made easy + - title_md: peptideshaker + description_md: PeptideShaker and SearchGUI + - title_md: pfamscan + description_md: Search a FASTA sequence against a library of Pfam HMM. + - title_md: pharokka + description_md: rapid standardised annotation tool for bacteriophage genomes and + metagenomes + - title_md: phyloseq + description_md: Handling and analysis of high-throughput microbiome census data + - title_md: phyml + description_md: PhyML is a phylogeny software based on the maximum-likelihood + principle. + - title_md: picrust + description_md: PICRUSt wrappers + - title_md: picrust2 + description_md: 'PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction + of Unobserved States' + - title_md: plasflow + description_md: PlasFlow - Prediction of plasmid sequences in metagenomic contigs. + - title_md: plasmidfinder + description_md: '"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"' + - title_md: plasmidspades + description_md: Genome assembler for assemblying plasmid + - title_md: polypolish + description_md: '"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."' + - title_md: prodigal + description_md: A protein-coding gene prediction software tool for bacterial and + archaeal genomes + - title_md: prokka + description_md: Rapid annotation of prokaryotic genomes + - title_md: promer + description_md: Aligns two sets of contigs and reports amino acid substitutions + between them + - title_md: proteinortho + description_md: Proteinortho is a tool to detect orthologous proteins/genes within + different species. + - title_md: pycoqc + description_md: QC metrics for ONT Basecalling + - title_md: pygenometracks + description_md: 'pyGenomeTracks: Standalone program and library to plot beautiful + genome browser tracks.' + - title_md: qiime_add_on + description_md: QIIME to perform microbial community analysis + - title_md: qiime_core + description_md: QIIME to perform microbial community analysis + - title_md: qualimap + description_md: 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. + - title_md: quast + description_md: Quast (Quality ASsessment Tool) evaluates genome assemblies. + - title_md: quickmerge + description_md: Merge long-read and hybrid assemblies to increase contiguity + - title_md: rRNA + description_md: Identification of ribosomal RNA genes in metagenomic fragments. + - title_md: racon + description_md: Consensus module for raw de novo DNA assembly of long uncorrected + reads. + - title_md: rasusa + description_md: Randomly subsample sequencing reads to a specified coverage + - title_md: raxml + description_md: RAxML - A Maximum Likelihood based phylogenetic inference + - title_md: read_it_and_keep + description_md: Rapid decontamination of SARS-CoV-2 sequencing reads + - title_md: reago + description_md: Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic + data. + - title_md: recentrifuge + description_md: '"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."' + - title_md: repeatexplorer2 + description_md: Tool for annotation of repeats from unassembled shotgun reads. + - title_md: roary + description_md: Roary the pangenome pipeline + - title_md: rseqc + description_md: an RNA-seq quality control package + - title_md: salmon + description_md: Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq and single-cell data. + - title_md: sarscov2formatter + description_md: sarscov2formatter custom script + - title_md: sarscov2summary + description_md: sarscov2summary custom script + - title_md: scoary + description_md: Scoary calculates the assocations between all genes in the accessory + genome and the traits. + - title_md: semibin + description_md: 'SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural + Networks' + - title_md: seqkit + description_md: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation + - title_md: seqprep + description_md: Tool for merging paired-end Illumina reads and trimming adapters. + - title_md: seqsero2 + description_md: Salmonella serotype prediction from genome sequencing data + - title_md: shorah + description_md: Reconstruct haplotypes using ShoRAH in amplicon mode + - title_md: shovill + description_md: Faster de novo assembly pipeline based around Spades + - title_md: sistr_cmd + description_md: SISTR in silico serotyping tool + - title_md: smallgenomeutilities + description_md: Set of utilities for manipulating small viral genome data. + - title_md: smalt + description_md: SMALT aligns DNA sequencing reads with a reference genome. + - title_md: snap + description_md: SNAP is a general purpose gene finding program suitable for both + eukaryotic and prokaryotic genomes. + - title_md: snippy + description_md: Contains the snippy tool for characterising microbial snps + - title_md: sonneityping + description_md: Scripts for parsing Mykrobe predict results for Shigella sonnei. + - title_md: sortmerna + description_md: SortMeRNA is a software designed to rapidly filter ribosomal RNA + fragments from metatransriptomic data produced by next-generation sequencers. + - title_md: spades + description_md: '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.' + - title_md: spotyping + description_md: SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping + from sequence reads + - title_md: sr_bowtie + description_md: bowtie wrapper tool to align small RNA sequencing reads + - title_md: srst2 + description_md: Short Read Sequence Typing for Bacterial Pathogens + - title_md: srst2 + description_md: SRST2 Short Read Sequence Typing for Bacterial Pathogens + - title_md: staramr + description_md: Scan genome contigs against the ResFinder, PlasmidFinder, and + PointFinder antimicrobial resistance databases. + - title_md: stringmlst + description_md: Rapid and accurate identification of the sequence type (ST) + - title_md: structure + description_md: for using multi-locus genotype data to investigate population + structure. + - title_md: suite_qiime2__alignment + description_md: .nan + - title_md: suite_qiime2__composition + description_md: .nan + - title_md: suite_qiime2__cutadapt + description_md: .nan + - title_md: suite_qiime2__dada2 + description_md: .nan + - title_md: suite_qiime2__deblur + description_md: .nan + - title_md: suite_qiime2__demux + description_md: .nan + - title_md: suite_qiime2__diversity + description_md: .nan + - title_md: suite_qiime2__diversity_lib + description_md: .nan + - title_md: suite_qiime2__emperor + description_md: .nan + - title_md: suite_qiime2__feature_classifier + description_md: .nan + - title_md: suite_qiime2__feature_table + description_md: .nan + - title_md: suite_qiime2__fragment_insertion + description_md: .nan + - title_md: suite_qiime2__longitudinal + description_md: .nan + - title_md: suite_qiime2__metadata + description_md: .nan + - title_md: suite_qiime2__phylogeny + description_md: .nan + - title_md: suite_qiime2__quality_control + description_md: .nan + - title_md: suite_qiime2__quality_filter + description_md: .nan + - title_md: suite_qiime2__rescript + description_md: .nan + - title_md: suite_qiime2__sample_classifier + description_md: .nan + - title_md: suite_qiime2__taxa + description_md: .nan + - title_md: suite_qiime2__vsearch + description_md: .nan + - title_md: suite_qiime2_core + description_md: .nan + - title_md: suite_qiime2_core__tools + description_md: .nan + - title_md: t2ps + description_md: Draw phylogeny + - title_md: t2t_report + description_md: Summarize taxonomy + - title_md: t_coffee + description_md: T-Coffee + - title_md: taxonomy_krona_chart + description_md: Krona pie chart from taxonomic profile + - title_md: tb-profiler + description_md: Processes M. tuberculosis sequence data to infer strain type and + identify known drug resistance markers. + - title_md: tooldistillator + description_md: ToolDistillator extract and aggregate information from different + tool outputs to JSON parsable files + - title_md: transit + description_md: TRANSIT + - title_md: transtermhp + description_md: Finds rho-independent transcription terminators in bacterial genomes + - title_md: trim_galore + description_md: Trim Galore adaptive quality and adapter trimmer + - title_md: trycycler + description_md: Trycycler toolkit wrappers + - title_md: unicycler + description_md: Unicycler is a hybrid assembly pipeline for bacterial genomes. + - title_md: unipept + description_md: Unipept retrieves metaproteomics information + - title_md: uniprotxml_downloader + description_md: Download UniProt proteome in XML or fasta format + - title_md: usher + description_md: UShER toolkit wrappers + - title_md: valet + description_md: A pipeline for detecting mis-assemblies in metagenomic assemblies. + - title_md: vapor + description_md: Classify Influenza samples from raw short read sequence data + - title_md: varvamp + description_md: Variable VirusAMPlicons (varVAMP) is a tool to design primers + for highly diverse viruses + - title_md: vegan + description_md: an R package fo community ecologist + - title_md: velvet + description_md: de novo genomic assembler specially designed for short read sequencing + technologies + - title_md: velvet_optimiser + description_md: Automatically optimize Velvet assemblies + - title_md: virAnnot + description_md: virAnnot wrappers + - title_md: vsearch + description_md: VSEARCH including searching, clustering, chimera detection, dereplication, + sorting, masking and shuffling of sequences. + - title_md: wtdbg + description_md: WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads + assembly. From 314ff1670fd6ef28a6ee91bbb4cafd284e6b7d1e Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Fri, 6 Dec 2024 08:11:49 +0100 Subject: [PATCH 21/38] changing to the new structure of excalidraw, content still need to be filled --- .../microgalaxy/lab/sections/1_beginner.yml | 233 ------------------ .../1_data_import_and_preparation.yml | 110 +++++++++ .../lab/sections/2_intermediate.yml | 36 --- .../lab/sections/2_microbial isolates.yml | 38 +++ .../microgalaxy/lab/sections/3_microbiome.yml | 38 +++ .../lab/sections/{5_tools.yml => 4_tools.yml} | 0 .../{3_advanced.yml => 5_workflows.yml} | 3 +- .../lab/sections/6_support_and_help.yml | 55 +++++ .../{4_community.yml => 7_community.yml} | 17 +- 9 files changed, 252 insertions(+), 278 deletions(-) delete mode 100644 communities/microgalaxy/lab/sections/1_beginner.yml create mode 100644 communities/microgalaxy/lab/sections/1_data_import_and_preparation.yml delete mode 100644 communities/microgalaxy/lab/sections/2_intermediate.yml create mode 100644 communities/microgalaxy/lab/sections/2_microbial isolates.yml create mode 100644 communities/microgalaxy/lab/sections/3_microbiome.yml rename communities/microgalaxy/lab/sections/{5_tools.yml => 4_tools.yml} (100%) rename communities/microgalaxy/lab/sections/{3_advanced.yml => 5_workflows.yml} (99%) create mode 100644 communities/microgalaxy/lab/sections/6_support_and_help.yml rename communities/microgalaxy/lab/sections/{4_community.yml => 7_community.yml} (55%) diff --git a/communities/microgalaxy/lab/sections/1_beginner.yml b/communities/microgalaxy/lab/sections/1_beginner.yml deleted file mode 100644 index d4aac6a8..00000000 --- a/communities/microgalaxy/lab/sections/1_beginner.yml +++ /dev/null @@ -1,233 +0,0 @@ -id: beginner -title: Learn to use Galaxy for microbial data analysis -tabs: - - id: learning_pathway - title: Learning pathways - heading_md: > - Connected tutorials to train you to perform single-cell analysis fast! - content: - - title_md: Introduction to Galaxy and Sequence analysis - description_md: > - This learning path aims to teach you the basics of Galaxy and analysis of sequencing data. You will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences. - - New to Galaxy and/or the field of genomics? Follow this {gtn modal}[learning path to get familiar with the basics](https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html)! - button_link: https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html - button_icon: tutorial - button_tip: Go to learning pathway - - title_md: Genome annotation for prokaryotes - description_md: > - Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo. - Check out the {gtn modal}[Genome annotation for prokaryotes learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html). - button_link: https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html - button_icon: tutorial - button_tip: Go to learning pathway - - title_md: Detection of AMR genes in bacterial genomes - description_md: > - This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy. - - Check out the {gtn modal}[Detection of AMR genes in bacterial genomes learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html). - button_link: https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html - button_icon: tutorial - button_tip: Go to learning pathway - - title_md: Metagenomics data processing and analysis for microbiome - description_md: > - This learning path aims to teach you the basics of Galaxy and analysis of metagenomics data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of microbiome data analysis: quality control, taxonomic profiling, taxonomic binning, assembly, functional profiling, and also some applications - - Check out the {gtn modal}[Metagenomics data processing and analysis for microbiome learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html). - button_link: https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html - button_tip: Go to learning pathway - button_icon: tutorial - - title_md: Clinical metaproteomics workflows within Galaxy - description_md: > - This learning path aims to teach you the basics of how to perform metaproteomics analysis of the clinical data within the Galaxy platform. You will learn how to use Galaxy for analysis and will be guided through the most common first steps of any metaproteomics database generation to searching the database, verifying the proteins/peptides, and data analysis. - - Check out the {gtn modal}[Clinical metaproteomics workflows within Galaxy learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html). - button_link: https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html - button_tip: View training menu - button_icon: tutorial - - - id: bacterial_genomics_tutorial - title: Bacterial genomics tutorials - heading_md: > - Using public data is free! Learn how to retrieve data from common sources. - content: - - title_md: Importing files from the Single Cell Expression Atlas - description_md: > - You can import data directly from the Single Cell Expression Atlas with one tool. You will need an **experiment accession** ID, which you can find by browsing experiments at the [EBI Atlas site](https://www.ebi.ac.uk/gxa/sc/experiments). Input that **experiment accession** ID in the *Tool Parameters* box when of the following tool. Then **Run tool** to get your matrix! - EBI SCXA Data Retrieval - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fretrieve_scxa%2fretrieve_scxa" - button_icon: run - button_tip: Run tool - - title_md: Importing from public atlases - Tutorial - description_md: > - You can learn more by following our dedicated to tutorial for importing files from public atlases. - button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/tutorial.html - button_icon: tutorial - button_tip: View tutorial - - title_md: Importing from NCBI/GEO - description_md: > - Where there isn't a specific tool for retrieving data, you can nevertheless import and reformat data from the commonly used NCBI/GEO repository with the following tutorial. - button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html - button_icon: tutorial - button_tip: View tutorial - - title_md: Importing 10X Files - description_md: > - You can find many tools for importing 10X formatted data into target datatypes. - Scanpy Read10x - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_read_10x%2fscanpy_read_10x" - button_icon: run - button_tip: Run tool - - title_md: Seurat Read10x - description_md: > - Import 10X formatted data into a Seurat object. Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_read10x%2fseurat_read10x" - button_icon: run - button_tip: Run tool - - title_md: DropletUtils Read10x - description_md: > - DropletUtils 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. - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fdropletutils_read_10x%2fdropletutils_read_10x" - button_icon: run - button_tip: Run tool - - - id: data_convert - title: Converting datatypes - heading_md: > - Single-cell data comes in many formats. - Here we show a few key tools in Galaxy for converting and manipulating objects in Galaxy. - content: - - title_md: SCEasy Converter - description_md: > - This tool allows you to convert between the following formats: - - - `hdf5` (AnnData/Loom) - - `rds` (Seurat) - - `rdata.sce` (Single Cell Experiment) - - `h5` (Seurat) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/sceasy_convert%2fsceasy_convert" - button_icon: run - button_tip: Run tool - - title_md: Manipulate AnnData - description_md: > - Under the parameter `Function to manipulate the object` you'll find key manipulations for AnnData, such as: - - - `Concatenate along the observations axis` for combining AnnData objects together - - `Transpose the data matrix` for help with converting formats - - `Filter observations or variables` for refining or subsetting your dataset - - `Adding annotations` and `Rename categories` for manipulating metadata - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/anndata_manipulate%2fanndata_manipulate" - button_icon: run - button_tip: Run tool - - title_md: AnnData Operations - description_md: > - This tool allows you to flag genes (such as mitochondrial genes) as well as change names in the metadata. - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fanndata_ops%2fanndata_ops" - button_icon: run - button_tip: Run tool - - title_md: Data conversion training - description_md: > - You can also explore our dedicated tutorial on single-cell data conversion. - button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" - button_icon: tutorial - button_tip: View tutorial - - - id: data_viz - title: Visualising Data - heading_md: > - There are a few key tools for visualising single-cell data in Galaxy. - content: - - title_md: Plot with Scanpy - description_md: > - This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots. - inputs: - - label: Single cell data - datatypes: - - hdf5 (AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/scanpy_plot%2fscanpy_plot" - button_icon: run - button_tip: Run tool - - title_md: Scanpy PlotEmbed - description_md: > - This tool allows you to plot embeddings like UMAPs. - inputs: - - label: Single cell data - datatypes: - - hdf5 (AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_plot_embed%2fscanpy_plot_embed" - button_icon: run - button_tip: Run tool - - title_md: Scanpy PlotTrajectory - description_md: > - This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object. - inputs: - - label: Single cell data - datatypes: - - hdf5 (AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxi%2fscanpy_plot_trajectory/scanpy_plot_trajectory" - button_icon: run - button_tip: Run tool - - title_md: Scanpy Plot dimension reduction - description_md: > - This tool allows you to plot embeddings such as PCA, UMAP, and tSNE. - inputs: - - label: Single cell data - datatypes: - - rds (Seurat object) - - rdata.sce (Single Cell Experiment) - - h5 (Seurat) - - hdf5 (Loom/AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_dim_plot%2fseurat_dim_plot" - button_icon: run - button_tip: Run tool - - title_md: Plot with Seurat - description_md: > - This tool allows you to plot gene expressions, such as with Violin Plots. - inputs: - - label: Single cell data - datatypes: - - rds (Seurat object) - - rdata.sce (Single Cell Experiment) - - h5 (Seurat) - - hdf5 (Loom/AnnData) - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_plot%2fseurat_plot" - button_icon: run - button_tip: Run tool - - - id: help - title: Help - content: - - title_md: Single Cell help forum - description_md: > - Of course! Check out the Galaxy Project - [Single cell help forum](https://help.galaxyproject.org/tag/scrna) - - title_md: Troubleshooting errors - description_md: > - Find specific advice for - {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) - on the GTN. - - title_md: Can I upload sensitive data? - description_md: > - No, please do not upload personal or sensitive, such as human health or clinical data. Please see our - [Privacy Policy]({{ data_policy_url }}) - page for definitions of sensitive and health-related information. - - Please also make sure you have read our - [Terms of Service]({{ terms_url }}), - which covers hosting and analysis of research data. - - title_md: Is my data private? - description_md: > - Please read our - [Privacy Policy]({{ data_policy_url }}) - for information on your personal data and any data that you upload. - - title_md: How can I increase my storage quota? - description_md: > - Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request. - button_md: Request - button_link: "{{ quota_request_url }}" - exclude_from: - - usegalaxy.org - - title_md: Galaxy {{ site_name }} support - description_md: > - Any user of Galaxy {{ site_name }} can request support online! - button_md: Request support - button_link: "{{ support_url }}" diff --git a/communities/microgalaxy/lab/sections/1_data_import_and_preparation.yml b/communities/microgalaxy/lab/sections/1_data_import_and_preparation.yml new file mode 100644 index 00000000..0c892cde --- /dev/null +++ b/communities/microgalaxy/lab/sections/1_data_import_and_preparation.yml @@ -0,0 +1,110 @@ +id: data +title: Data import and preparation +tabs: + - id: tools + title: Tools + heading_md: > + Common tools are listed here, or search for more in the full tool panel to the left. + content: + - title_md: Import data to Galaxy + description_md: > + Standard upload of data to Galaxy, from your computer or from the web. + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1" + - title_md: FastQC - sequence quality reports + description_md: > +

+ Before using your sequencing data, it's important to ensure that + the data quality is sufficient for your analysis. +

+ inputs: + - datatypes: + - fastq + - bam + - sam + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc" + - title_md: FastP - sequence quality reports, trimming & filtering + description_md: > +

+ Faster run than FastQC, this tool can also trim reads and filter by quality. +

+ inputs: + - datatypes: + - fastq + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffastp%2Ffastp" + - title_md: NanoPlot - visualize Oxford Nanopore data + description_md: > +

+ A plotting suite for Oxford Nanopore sequencing data and alignments. +

+ inputs: + - datatypes: + - fastq + - fasta + - vcf_bgzip + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnanoplot%2Fnanoplot" + - title_md: GenomeScope - estimate genome size + description_md: > +

+ A set of metrics and graphs to visualize genome size and complexity prior to assembly. +

+ inputs: + - datatypes: + - tabular + label: Output from Meryl or Jellyfish histo + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgenomescope%2Fgenomescope" + - title_md: Meryl - count kmers + description_md: > +

+ Prepare kmer count histogram for input to GenomeScope. +

+ inputs: + - datatypes: + - fastq + - fasta + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmeryl%2Fmeryl" + + - id: workflows + title: Workflows + heading_md: > + A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below. + Learn more. + content: + - title_md: Data QC + description_md: > +

+ Report statistics from sequencing reads.

Tools: nanoplot fastqc multiqc +

+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222" + view_link: https://workflowhub.eu/workflows/222 + view_tip: View in WorkflowHub + button_tip: Import to Galaxy AU + - title_md: Kmer counting to estimate genome size + description_md: > +

+ Estimates genome size and heterozygosity based on counts of kmers.

Tools: meryl genomescope +

+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=223" + view_link: https://workflowhub.eu/workflows/223 + view_tip: View in WorkflowHub + button_tip: Import to Galaxy AU + - title_md: Trim and filter reads + description_md: > +

+ Trims and filters raw sequence reads according to specified settings.

Tools: fastp +

+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=224" + view_link: https://workflowhub.eu/workflows/224 + view_tip: View in WorkflowHub + button_tip: Import to Galaxy AU + + - id: tutorials + title: Tutorials + heading_md: > + + content: [] + + - id: faq + title: FAQ + heading_md: > + + content: [] \ No newline at end of file diff --git a/communities/microgalaxy/lab/sections/2_intermediate.yml b/communities/microgalaxy/lab/sections/2_intermediate.yml deleted file mode 100644 index f9cc27ae..00000000 --- a/communities/microgalaxy/lab/sections/2_intermediate.yml +++ /dev/null @@ -1,36 +0,0 @@ -id: intermediate -title: Advanced analysis -tabs: - - id: workflows - title: Multiomic Analyses - content: - - title_md: These tutorials use different methods to analyse scRNA-seq samples. - description_md: > - {gtn modal}[Learn more](https://training.galaxyproject.org/training-material/topics/single-cell/#st-end-to-end/) - - - - - id: deconvolution - title: Deconvolution - heading_md: > - These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference - These tutorials use different methods to analyse scRNA-seq samples. - Learn more. - content: [] - - - id: tips - title: Tips, tricks & other hints - heading_md: > - These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference - These tutorials use different methods to analyse scRNA-seq samples. - Learn more. - content: - - title_md: About these workflows - description_md: > - Hello! Mehmet working here - button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html#tip-creating-a-new-history - button_tip: View tutorial - button_icon: tutorial - - title_md: Spare space for another GTN - description_md: > - More GTN diff --git a/communities/microgalaxy/lab/sections/2_microbial isolates.yml b/communities/microgalaxy/lab/sections/2_microbial isolates.yml new file mode 100644 index 00000000..f6cc84cd --- /dev/null +++ b/communities/microgalaxy/lab/sections/2_microbial isolates.yml @@ -0,0 +1,38 @@ +id: isolates +title: Microbial isolates +tabs: + - id: workflows + title: Workflows + heading_md: > + + content: [] + + - id: tutorials + title: Tutorials + heading_md: > + + content: [] + + - id: pathways + title: Learning pathways + heading_md: > + Connected tutorials to train you to perform microbial data analysis fast!. + content: + - title_md: Introduction to Galaxy and Sequence analysis + description_md: > + New to Galaxy and/or the field of genomics? In this learing pathway, you will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences. + button_link: + - title_md: Genome annotation for prokaryotes + description_md: > + + button_link: + - title_md: Detection of AMR genes in bacterial genomes + description_md: > + + button_link: + + - id: faq + title: FAQ + heading_md: > + + content: [] \ No newline at end of file diff --git a/communities/microgalaxy/lab/sections/3_microbiome.yml b/communities/microgalaxy/lab/sections/3_microbiome.yml new file mode 100644 index 00000000..5e339542 --- /dev/null +++ b/communities/microgalaxy/lab/sections/3_microbiome.yml @@ -0,0 +1,38 @@ +id: microbiome +title: Microbiome +tabs: + - id: workflows + title: Workflows + heading_md: > + + content: [] + + - id: tutorials + title: Tutorials + heading_md: > + + content: [] + + - id: pathways + title: Learning pathways + heading_md: > + Connected tutorials to train you to perform microbial data analysis fast!. + content: + - title_md: Introduction to Galaxy and Sequence analysis + description_md: > + New to Galaxy and/or the field of genomics? In this learing pathway, you will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences. + button_link: + - title_md: Metagenomics data processing and analysis for microbiome + description_md: > + + button_link: + - title_md: Clinical metaproteomics workflows within Galaxy + description_md: > + + button_link: + + - id: faq + title: FAQ + heading_md: > + + content: [] \ No newline at end of file diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/4_tools.yml similarity index 100% rename from communities/microgalaxy/lab/sections/5_tools.yml rename to communities/microgalaxy/lab/sections/4_tools.yml diff --git a/communities/microgalaxy/lab/sections/3_advanced.yml b/communities/microgalaxy/lab/sections/5_workflows.yml similarity index 99% rename from communities/microgalaxy/lab/sections/3_advanced.yml rename to communities/microgalaxy/lab/sections/5_workflows.yml index bf837dac..b13d1053 100644 --- a/communities/microgalaxy/lab/sections/3_advanced.yml +++ b/communities/microgalaxy/lab/sections/5_workflows.yml @@ -1,4 +1,4 @@ -id: advanced +id: workflows title: Workflows tabs: - id: workflows1 @@ -49,6 +49,7 @@ tabs: button_link: "https://workflowhub.eu/search?q=microgalaxy+galaxy" button_md: 🔗 button_tip: Visit WorkflowHub + - id: workflows3 title: Community workflows heading_md: > diff --git a/communities/microgalaxy/lab/sections/6_support_and_help.yml b/communities/microgalaxy/lab/sections/6_support_and_help.yml new file mode 100644 index 00000000..b8cf43d4 --- /dev/null +++ b/communities/microgalaxy/lab/sections/6_support_and_help.yml @@ -0,0 +1,55 @@ +id: support +title: Support & Help +tabs: + - id: help + title: Help + heading_md: > + You can browse through workflows before that have been reviewed by scientists. + content: + - title_md: Troubleshooting errors + description_md: > + Find specific advice for + {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) + on the GTN. + - title_md: Galaxy [Australia/France/EU/..] Support + description_md: > + Any user of Galaxy [Australia/..] can request support online! + button_md: Request support + button_link: "{{ support_url }}" + - title_md: General Galaxy support + description_md: > + ... + button_link: "{{ url }}" + button_tip: .. + button_icon: .. + - title_md: microGalaxy chat room + description_md: > + Of course! Check out the microGalaxy Matrix channel + [microGalaxy Matrix](https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im) + button_link: "{{ url }}" + button_tip: .. + button_icon: .. + - title_md: Can I upload sensitive data? + description_md: > + No, please do not upload personal or sensitive, such as human health or clinical data. Please see our + [Privacy Policy]({{ data_policy_url }}) + page for definitions of sensitive and health-related information. + + Please also make sure you have read our + [Terms of Service]({{ terms_url }}), + which covers hosting and analysis of research data. + - title_md: Is my data private? + description_md: > + Please read our + [Privacy Policy]({{ data_policy_url }}) + for information on your personal data and any data that you upload. + + - id: request + title: Request + - title_md: How can I increase my storage quota? + description_md: > + Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request. + button_md: Request + button_link: "{{ quota_request_url }}" + exclude_from: + - usegalaxy.org diff --git a/communities/microgalaxy/lab/sections/4_community.yml b/communities/microgalaxy/lab/sections/7_community.yml similarity index 55% rename from communities/microgalaxy/lab/sections/4_community.yml rename to communities/microgalaxy/lab/sections/7_community.yml index 16349ee3..b1f9e8a4 100644 --- a/communities/microgalaxy/lab/sections/4_community.yml +++ b/communities/microgalaxy/lab/sections/7_community.yml @@ -6,22 +6,23 @@ tabs: content: - title_md: Chat with other users description_md: > - Check out some suggestions on how you can - {gtn modal}[connect with the community](https://training.galaxyproject.org/training-material/topics/single-cell/faqs/user_community_join.html). + Of course! Check out the microGalaxy Matrix channel + [microGalaxy Matrix](https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im) - title_md: Join our community! description_md: > This Galaxy space is the result of hard, collaborative work by many contributors . - It is maintained by the [Galaxy Single-cell & sPatial Omics **SPOC** Community of Practice](https://galaxyproject.org/community/sig/singlecell/). + It is maintained by the microGalaxy Community of Practice. - This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make single-cell & spatial omics analysis easier. + This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make microvial data analysis easier. - Check out our site and join our community! + Check out our site and join our community via [microGalaxy mailing list](https://lists.galaxyproject.org/lists/microgalaxy@lists.galaxyproject.org)! - button_link: "https://galaxyproject.org/community/sig/singlecell/" - button_md: 🖖🏽 - button_tip: Visit SPOC + button_link: "" + button_md: + button_tip: Visit microGalaxy + - id: governance title: How is the Galaxy Community organised? content: From 5225642e5d6a684e0a9e23e2fa4c200fd48c57ad Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 11 Dec 2024 11:57:08 +0100 Subject: [PATCH 22/38] changing base and usegalaxy servers yml files --- communities/microgalaxy/lab/CONTRIBUTORS | 3 +- communities/microgalaxy/lab/base.yml | 35 +-- .../lab/sections/6_support_and_help.yml | 14 +- .../microgalaxy/lab/sections/7_community.yml | 2 +- .../lab/static/logo_single_cell.svg | 276 ------------------ .../lab/static/microgalaxy-logo.png | Bin 0 -> 21073 bytes communities/microgalaxy/lab/usegalaxy.eu.yml | 12 +- .../microgalaxy/lab/usegalaxy.org.au.yml | 12 +- .../usegalaxy.org.au/templates/footer.html | 2 +- communities/microgalaxy/lab/usegalaxy.org.yml | 12 +- 10 files changed, 46 insertions(+), 322 deletions(-) delete mode 100644 communities/microgalaxy/lab/static/logo_single_cell.svg create mode 100644 communities/microgalaxy/lab/static/microgalaxy-logo.png diff --git a/communities/microgalaxy/lab/CONTRIBUTORS b/communities/microgalaxy/lab/CONTRIBUTORS index f1d71278..f26526af 100644 --- a/communities/microgalaxy/lab/CONTRIBUTORS +++ b/communities/microgalaxy/lab/CONTRIBUTORS @@ -1,3 +1,4 @@ # If GitHub username, name and avatar will be fetched and displayed bebatut -zierep \ No newline at end of file +zierep +EngyNasr \ No newline at end of file diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index f48401be..befaabe6 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -7,37 +7,35 @@ # To make the content more generic and reusable across sites # These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!" -site_name: Australia +site_name: European lab_name: microGalaxy Lab analysis_name: microGalaxy -nationality: Australian +nationality: Europeam # Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.org -subdomain: singlecell -root_domain: usegalaxy.org +galaxy_base_url: https://microgalaxy.usegalaxy.eu +subdomain: microGalaxy +root_domain: usegalaxy.eu # This will enable a feedback form on the webpage: # feedback_email: help@mygalaxy.org support_url: https://help.galaxyproject.org -# quota_request_url: https://help.galaxyproject.org +quota_request_url: https://help.galaxyproject.org data_policy_url: https://usegalaxy.org/static/terms.html terms_url: https://usegalaxy.org/static/terms.html help_links: - title: General Galaxy support url: https://galaxyproject.org/support/ - - title: Single Cell help forum - url: https://help.galaxyproject.org/tag/single-cell + - title: microGalaxy help forum + url: https://help.galaxyproject.org/tag/microGalaxy - title: General Galaxy help forum url: https://help.galaxyproject.org - title: Galaxy Training Network Slack workspace url: https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg - - title: Single cell Slack channel (#single-cell-users) - url: https://gtnsmrgsbord.slack.com/archives/C06PBRR40D7 - - title: Single cell user community chat room (Same channel but using Matrix/Element) - url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - title: microGalaxy user community chat room (Same channel but using Matrix/Element) + url: https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im - title: Galaxy Training Community chat url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im - title: Usegalaxy.org chat @@ -49,7 +47,7 @@ conclusion_extra_md: "" # ----------------------------------------------------------------------------- # Custom content relative to this file URL -header_logo: static/logo_single_cell.svg +header_logo: static/microGalaxy-logo.png custom_css: static/custom.css intro_md: templates/intro.html conclusion_md: templates/conclusion.html @@ -61,9 +59,12 @@ footer_md: templates/footer.html # 1. Relative to this file URL # 2. Full URL to fetch globally centralized content sections: - - sections/1_beginner.yml - - sections/3_advanced.yml - - sections/4_community.yml - - sections/5_tools.yml + - sections/1_data_import_and_preparation.yml + - sections/2_microbial_isolates.yml + - sections/3_microbiome.yml + - sections/4_tools.yml + - sections/5_workflows.yml + - sections/6_support_and_help.yml + - sections/7_community.yml # ----------------------------------------------------------------------------- diff --git a/communities/microgalaxy/lab/sections/6_support_and_help.yml b/communities/microgalaxy/lab/sections/6_support_and_help.yml index b8cf43d4..96faff79 100644 --- a/communities/microgalaxy/lab/sections/6_support_and_help.yml +++ b/communities/microgalaxy/lab/sections/6_support_and_help.yml @@ -19,16 +19,16 @@ tabs: - title_md: General Galaxy support description_md: > ... - button_link: "{{ url }}" - button_tip: .. - button_icon: .. + button_link: "{{ galaxy_base_url }}" + button_tip: + button_icon: - title_md: microGalaxy chat room description_md: > Of course! Check out the microGalaxy Matrix channel [microGalaxy Matrix](https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im) - button_link: "{{ url }}" - button_tip: .. - button_icon: .. + button_link: + button_tip: + button_icon: - title_md: Can I upload sensitive data? description_md: > No, please do not upload personal or sensitive, such as human health or clinical data. Please see our @@ -51,5 +51,3 @@ tabs: Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request. button_md: Request button_link: "{{ quota_request_url }}" - exclude_from: - - usegalaxy.org diff --git a/communities/microgalaxy/lab/sections/7_community.yml b/communities/microgalaxy/lab/sections/7_community.yml index b1f9e8a4..17447870 100644 --- a/communities/microgalaxy/lab/sections/7_community.yml +++ b/communities/microgalaxy/lab/sections/7_community.yml @@ -22,7 +22,7 @@ tabs: button_link: "" button_md: button_tip: Visit microGalaxy - + - id: governance title: How is the Galaxy Community organised? content: diff --git a/communities/microgalaxy/lab/static/logo_single_cell.svg b/communities/microgalaxy/lab/static/logo_single_cell.svg deleted file mode 100644 index 43540c2b..00000000 --- a/communities/microgalaxy/lab/static/logo_single_cell.svg +++ /dev/null @@ -1,276 +0,0 @@ - - - - - - - - - - - - - - - - image/svg+xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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z(Dt^$HR46yzIo|NjhSlyR(W0e<=II9y>OhatHxP+wg!C*>{Se^iiT^Z>a8NETz6kQ zmCp3=QX`MAq?$XRB5S5C`#53UU|UqL6wR7xuilH2v~a&x(0A$5V|S5~93u7X;|tcO z4nrl&cuR4umWV&lcU}`4pw9r%#{pdS55eq6e31$cD+$*1*~#-I3hl3AVAm4R$5+MjJ+I+>KA<;(gOt9e8T54hhl`{z zi)OEIg(NT26IcD4gOdnk0l_e^FYQ+VyR zomAUsYoThjil>>$b#Z#fQ!#y0lO787!_E_R6gQXos%ct^yQ>x?FTgOAh)8jhe zeC&K~@xf7f!3{pQdiwWU^!XB3`lOC{g4F|09FyfdZhpA%>QhPyg@p;%zJ?r&Nj!)a zPjB^INDt7z7W%9~+yKTJ*avU(s0f*>1+XS}DHwX0{`2ZA67N~4rSfE0t(zTvo15ClOs z7Z0RzMi!e=gzhe7AUf4#tY0NbItEt|f*{D|;u7N8(sreZxOxx-LD>uXOCONNECT - + \ No newline at end of file diff --git a/communities/microgalaxy/lab/usegalaxy.org.yml b/communities/microgalaxy/lab/usegalaxy.org.yml index 63934752..d04ea4fd 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.yml +++ b/communities/microgalaxy/lab/usegalaxy.org.yml @@ -13,22 +13,22 @@ site_name: "" # ? nationality: "" # Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://singlecell.usegalaxy.org -subdomain: singlecell +galaxy_base_url: https://microGalaxy.usegalaxy.org +subdomain: microGalaxy root_domain: usegalaxy.org # This will enable a feedback form on the webpage: # feedback_email: help@mygalaxy.org help_links: - - title: Single Cell community help forum - url: https://usegalaxy-eu.github.io/scrna + - title: microGalaxy community help forum + url: https://usegalaxy-eu.github.io/microGalaxy - title: General Galaxy support url: https://galaxyproject.org/support/ - title: General Galaxy help forum url: https://help.galaxyproject.org - - title: Single cell Galaxy user community chat room - url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im + - title: microGalaxy Galaxy user community chat room + url: https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im - title: Galaxy Training Community chat url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im - title: Usegalaxy.org chat From ed01a19fe581e3d2e6b13b89481edd7c41229682 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 11 Dec 2024 12:00:42 +0100 Subject: [PATCH 23/38] correcting file name --- .../{2_microbial isolates.yml => 2_microbial_isolates.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename communities/microgalaxy/lab/sections/{2_microbial isolates.yml => 2_microbial_isolates.yml} (100%) diff --git a/communities/microgalaxy/lab/sections/2_microbial isolates.yml b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml similarity index 100% rename from communities/microgalaxy/lab/sections/2_microbial isolates.yml rename to communities/microgalaxy/lab/sections/2_microbial_isolates.yml From ace6a536dbf7c7a59d77fe9c038e83c189c79672 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 11 Dec 2024 12:07:21 +0100 Subject: [PATCH 24/38] solving linting errors --- communities/microgalaxy/lab/sections/6_support_and_help.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/communities/microgalaxy/lab/sections/6_support_and_help.yml b/communities/microgalaxy/lab/sections/6_support_and_help.yml index 96faff79..9bc358d6 100644 --- a/communities/microgalaxy/lab/sections/6_support_and_help.yml +++ b/communities/microgalaxy/lab/sections/6_support_and_help.yml @@ -46,6 +46,7 @@ tabs: - id: request title: Request + content: - title_md: How can I increase my storage quota? description_md: > Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request. From 098252fc2252aa063b52f03fb04eca721126d7dc Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 11 Dec 2024 13:14:35 +0100 Subject: [PATCH 25/38] changing 2 links to microGalaxy --- communities/microgalaxy/lab/templates/conclusion.html | 4 ++-- .../microgalaxy/lab/usegalaxy.eu/templates/footer.html | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/communities/microgalaxy/lab/templates/conclusion.html b/communities/microgalaxy/lab/templates/conclusion.html index b751908f..ab554351 100644 --- a/communities/microgalaxy/lab/templates/conclusion.html +++ b/communities/microgalaxy/lab/templates/conclusion.html @@ -18,10 +18,10 @@

News and Events

- +
- +
diff --git a/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html index 0ff9c101..e4a8f7ad 100644 --- a/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html +++ b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html @@ -42,7 +42,7 @@

- Edit this page on GitHub + Edit this page on GitHub   From c066cb6e335f13d72e367b7cd61c57df1f416eec Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 11 Dec 2024 13:17:41 +0100 Subject: [PATCH 26/38] updating with microGalaxy logo --- communities/microgalaxy/lab/base.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index befaabe6..74c9fe91 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -47,7 +47,7 @@ conclusion_extra_md: "" # ----------------------------------------------------------------------------- # Custom content relative to this file URL -header_logo: static/microGalaxy-logo.png +header_logo: static/microgalaxy-logo.png custom_css: static/custom.css intro_md: templates/intro.html conclusion_md: templates/conclusion.html From fea11befb0aee657865164289d79768383ddc121 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 11 Dec 2024 13:46:39 +0100 Subject: [PATCH 27/38] changing news and events source link --- communities/microgalaxy/lab/base.yml | 2 +- communities/microgalaxy/lab/templates/conclusion.html | 6 +++--- communities/microgalaxy/lab/usegalaxy.eu.yml | 2 +- communities/microgalaxy/lab/usegalaxy.org.au.yml | 2 +- communities/microgalaxy/lab/usegalaxy.org.yml | 6 +++--- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index 74c9fe91..bbb12e54 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -1,5 +1,5 @@ # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/base.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/microgalaxy/base.yml # ----------------------------------------------------------------------------- # Use these variables in HTML templates like: diff --git a/communities/microgalaxy/lab/templates/conclusion.html b/communities/microgalaxy/lab/templates/conclusion.html index ab554351..9222c682 100644 --- a/communities/microgalaxy/lab/templates/conclusion.html +++ b/communities/microgalaxy/lab/templates/conclusion.html @@ -2,7 +2,7 @@

{% if help_links %} -

Single Cell and Spatial Omics community support

+

microGalaxy community support

    {% for link in help_links %}
  • @@ -18,10 +18,10 @@

    News and Events

    - +
    - +
diff --git a/communities/microgalaxy/lab/usegalaxy.eu.yml b/communities/microgalaxy/lab/usegalaxy.eu.yml index 7300a603..f35fb79d 100644 --- a/communities/microgalaxy/lab/usegalaxy.eu.yml +++ b/communities/microgalaxy/lab/usegalaxy.eu.yml @@ -1,7 +1,7 @@ # This content extends base.yml # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/usegalaxy.eu.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/microgalaxy/usegalaxy.eu.yml # ----------------------------------------------------------------------------- # Use these variables in HTML templates like: diff --git a/communities/microgalaxy/lab/usegalaxy.org.au.yml b/communities/microgalaxy/lab/usegalaxy.org.au.yml index 8cd77548..9bc9b482 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.au.yml +++ b/communities/microgalaxy/lab/usegalaxy.org.au.yml @@ -1,7 +1,7 @@ # This content extends base.yml # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/usegalaxy.org.au.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/microgalaxy/usegalaxy.org.au.yml # ----------------------------------------------------------------------------- # Use these variables in MD/HTML templates like: diff --git a/communities/microgalaxy/lab/usegalaxy.org.yml b/communities/microgalaxy/lab/usegalaxy.org.yml index d04ea4fd..6cb4c61c 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.yml +++ b/communities/microgalaxy/lab/usegalaxy.org.yml @@ -1,7 +1,7 @@ # This content extends base.yml # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/usegalaxy.org.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/microgalaxy/usegalaxy.org.yml # ----------------------------------------------------------------------------- # Use these variables in HTML templates like: @@ -13,7 +13,7 @@ site_name: "" # ? nationality: "" # Used for rendering tool/workflow links. Trailing '/' will be removed. -galaxy_base_url: https://microGalaxy.usegalaxy.org +galaxy_base_url: https://microgalaxy.usegalaxy.org subdomain: microGalaxy root_domain: usegalaxy.org @@ -22,7 +22,7 @@ root_domain: usegalaxy.org help_links: - title: microGalaxy community help forum - url: https://usegalaxy-eu.github.io/microGalaxy + url: https://usegalaxy-eu.github.io/microgalaxy - title: General Galaxy support url: https://galaxyproject.org/support/ - title: General Galaxy help forum From c7b6d48d47e65681e7414b9e75310ec23fe56307 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 11 Dec 2024 13:56:39 +0100 Subject: [PATCH 28/38] correcting links --- communities/microgalaxy/lab/usegalaxy.eu.yml | 4 ++-- .../microgalaxy/lab/usegalaxy.eu/templates/footer.html | 2 +- communities/microgalaxy/lab/usegalaxy.org.au.yml | 4 ++-- communities/microgalaxy/lab/usegalaxy.org.yml | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/communities/microgalaxy/lab/usegalaxy.eu.yml b/communities/microgalaxy/lab/usegalaxy.eu.yml index f35fb79d..f85c6883 100644 --- a/communities/microgalaxy/lab/usegalaxy.eu.yml +++ b/communities/microgalaxy/lab/usegalaxy.eu.yml @@ -1,7 +1,7 @@ # This content extends base.yml # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/microgalaxy/usegalaxy.eu.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/tree/main/communities/microgalaxy/usegalaxy.eu.yml # ----------------------------------------------------------------------------- # Use these variables in HTML templates like: @@ -26,7 +26,7 @@ terms_url: https://usegalaxy-eu.github.io/gdpr/tos.html help_links: - title: microGalaxy community help forum - url: https://usegalaxy-eu.github.io/microGalaxy + url: https://usegalaxy-eu.github.io/microgalaxy - title: General Galaxy support url: https://galaxyproject.org/support/ - title: Galaxy EU help forum diff --git a/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html index e4a8f7ad..148b200c 100644 --- a/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html +++ b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html @@ -42,7 +42,7 @@

- Edit this page on GitHub + Edit this page on GitHub   diff --git a/communities/microgalaxy/lab/usegalaxy.org.au.yml b/communities/microgalaxy/lab/usegalaxy.org.au.yml index 9bc9b482..03e61a34 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.au.yml +++ b/communities/microgalaxy/lab/usegalaxy.org.au.yml @@ -1,7 +1,7 @@ # This content extends base.yml # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/microgalaxy/usegalaxy.org.au.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/tree/main/communities/microgalaxy/usegalaxy.org.au.yml # ----------------------------------------------------------------------------- # Use these variables in MD/HTML templates like: @@ -32,7 +32,7 @@ help_links: - title: General Galaxy support url: https://galaxyproject.org/support/ - title: microGalaxy community help forum - url: https://usegalaxy-eu.github.io/microGalaxy + url: https://usegalaxy-eu.github.io/microgalaxy - title: General Galaxy help forum url: https://help.galaxyproject.org - title: microGalaxy Galaxy user community chat room diff --git a/communities/microgalaxy/lab/usegalaxy.org.yml b/communities/microgalaxy/lab/usegalaxy.org.yml index 6cb4c61c..cd301599 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.yml +++ b/communities/microgalaxy/lab/usegalaxy.org.yml @@ -1,7 +1,7 @@ # This content extends base.yml # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/microgalaxy/usegalaxy.org.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/tree/main/communities/microgalaxy/usegalaxy.org.yml # ----------------------------------------------------------------------------- # Use these variables in HTML templates like: From fafa4eec32ebdab893e8a85ad809f282f13f1079 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 11 Dec 2024 14:08:39 +0100 Subject: [PATCH 29/38] removing github microGalaxy link --- communities/microgalaxy/lab/base.yml | 2 -- communities/microgalaxy/lab/usegalaxy.eu.yml | 2 -- communities/microgalaxy/lab/usegalaxy.org.au.yml | 2 -- communities/microgalaxy/lab/usegalaxy.org.yml | 2 -- 4 files changed, 8 deletions(-) diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index bbb12e54..2f55b17c 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -28,8 +28,6 @@ terms_url: https://usegalaxy.org/static/terms.html help_links: - title: General Galaxy support url: https://galaxyproject.org/support/ - - title: microGalaxy help forum - url: https://help.galaxyproject.org/tag/microGalaxy - title: General Galaxy help forum url: https://help.galaxyproject.org - title: Galaxy Training Network Slack workspace diff --git a/communities/microgalaxy/lab/usegalaxy.eu.yml b/communities/microgalaxy/lab/usegalaxy.eu.yml index f85c6883..8343e551 100644 --- a/communities/microgalaxy/lab/usegalaxy.eu.yml +++ b/communities/microgalaxy/lab/usegalaxy.eu.yml @@ -25,8 +25,6 @@ data_policy_url: "#data-policy" terms_url: https://usegalaxy-eu.github.io/gdpr/tos.html help_links: - - title: microGalaxy community help forum - url: https://usegalaxy-eu.github.io/microgalaxy - title: General Galaxy support url: https://galaxyproject.org/support/ - title: Galaxy EU help forum diff --git a/communities/microgalaxy/lab/usegalaxy.org.au.yml b/communities/microgalaxy/lab/usegalaxy.org.au.yml index 03e61a34..fa7ccd02 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.au.yml +++ b/communities/microgalaxy/lab/usegalaxy.org.au.yml @@ -31,8 +31,6 @@ help_links: url: https://site.usegalaxy.org.au/request - title: General Galaxy support url: https://galaxyproject.org/support/ - - title: microGalaxy community help forum - url: https://usegalaxy-eu.github.io/microgalaxy - title: General Galaxy help forum url: https://help.galaxyproject.org - title: microGalaxy Galaxy user community chat room diff --git a/communities/microgalaxy/lab/usegalaxy.org.yml b/communities/microgalaxy/lab/usegalaxy.org.yml index cd301599..7ec421c2 100644 --- a/communities/microgalaxy/lab/usegalaxy.org.yml +++ b/communities/microgalaxy/lab/usegalaxy.org.yml @@ -21,8 +21,6 @@ root_domain: usegalaxy.org # feedback_email: help@mygalaxy.org help_links: - - title: microGalaxy community help forum - url: https://usegalaxy-eu.github.io/microgalaxy - title: General Galaxy support url: https://galaxyproject.org/support/ - title: General Galaxy help forum From e01d9cc6f3c8568a1f443819dac23d50ff60f7de Mon Sep 17 00:00:00 2001 From: Engy Nasr Date: Thu, 12 Dec 2024 11:49:20 +0100 Subject: [PATCH 30/38] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit applying comments Co-authored-by: BĂ©rĂ©nice Batut --- communities/microgalaxy/lab/base.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index 2f55b17c..ebcc19e8 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -10,7 +10,7 @@ site_name: European lab_name: microGalaxy Lab analysis_name: microGalaxy -nationality: Europeam +nationality: European # Used for rendering tool/workflow links. Trailing '/' will be removed. galaxy_base_url: https://microgalaxy.usegalaxy.eu From d4769c2b687ba86631e5a8cddfe9f347080f4751 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Thu, 12 Dec 2024 12:31:58 +0100 Subject: [PATCH 31/38] updating links --- communities/microgalaxy/lab/base.yml | 4 ++-- .../microgalaxy/lab/usegalaxy.eu/templates/footer.html | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index 2f55b17c..03d55058 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -1,5 +1,5 @@ # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/microgalaxy/base.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/tree/main/communities/microgalaxy/base.yml # ----------------------------------------------------------------------------- # Use these variables in HTML templates like: @@ -10,7 +10,7 @@ site_name: European lab_name: microGalaxy Lab analysis_name: microGalaxy -nationality: Europeam +nationality: European # Used for rendering tool/workflow links. Trailing '/' will be removed. galaxy_base_url: https://microgalaxy.usegalaxy.eu diff --git a/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html index 148b200c..f87a847b 100644 --- a/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html +++ b/communities/microgalaxy/lab/usegalaxy.eu/templates/footer.html @@ -42,7 +42,7 @@

- Edit this page on GitHub + Edit this page on GitHub   From d5989899efec3c39d52e218c5f9b65c0186b0ca0 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Thu, 12 Dec 2024 12:56:03 +0100 Subject: [PATCH 32/38] adding help links to the lab in the community section as a third tab --- .../microgalaxy/lab/sections/7_community.yml | 29 ++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/communities/microgalaxy/lab/sections/7_community.yml b/communities/microgalaxy/lab/sections/7_community.yml index 17447870..fcef5a9f 100644 --- a/communities/microgalaxy/lab/sections/7_community.yml +++ b/communities/microgalaxy/lab/sections/7_community.yml @@ -25,8 +25,35 @@ tabs: - id: governance title: How is the Galaxy Community organised? - content: heading_md: > Learn about the {gtn modal}[governance structure of Galaxy communities](https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html) on the GTN. content: [] + + - id: links + title: Galaxy Community support links + content: + - title_md: General support + description_md: > + [General Galaxy support](https://galaxyproject.org/support/) + - title_md: General help forum + description_md: > + [General Galaxy help forum](https://help.galaxyproject.org) + - title_md: Galaxy Training Network Slack workspace + description_md: > + [GTN Slack channel](https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg) + - title_md: Galaxy Training Network Community chat + description_md: > + [GTN Matrix channel](https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im) + - title_md: microGalaxy user community chat room (Same channel but using Matrix/Element) + description_md: > + [microGalaxy Matrix channel](https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im) + - title_md: American Galaxy Sever chat + description_md: > + [Usegalaxy.org chat](https://matrix.to/#/#galaxyproject_Lobby:gitter.im) + - title_md: Australian Galaxy Server chat + description_md: > + [Usegalaxy.org.au chat](https://site.usegalaxy.org.au/request) + - title_md: European Galaxy server chat + description_md: > + [Usegalaxy.eu chat](https://matrix.to/#/#usegalaxy-eu_Lobby:gitter.im) \ No newline at end of file From 22be3383eacc2b47211e7eab487b26d2de310e7b Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Thu, 12 Dec 2024 19:56:25 +0100 Subject: [PATCH 33/38] changing from links to buttons --- .../lab/sections/6_support_and_help.yml | 11 +++-- .../microgalaxy/lab/sections/7_community.yml | 43 ++++++++++++++----- .../microgalaxy/lab/templates/conclusion.html | 4 +- 3 files changed, 40 insertions(+), 18 deletions(-) diff --git a/communities/microgalaxy/lab/sections/6_support_and_help.yml b/communities/microgalaxy/lab/sections/6_support_and_help.yml index 9bc358d6..3906270e 100644 --- a/communities/microgalaxy/lab/sections/6_support_and_help.yml +++ b/communities/microgalaxy/lab/sections/6_support_and_help.yml @@ -11,22 +11,21 @@ tabs: Find specific advice for {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) on the GTN. - - title_md: Galaxy [Australia/France/EU/..] Support + - title_md: Galaxy [American/Australia/EU/France/..] Support description_md: > - Any user of Galaxy [Australia/..] can request support online! + Any user of Galaxy [American/Australia/EU/France/..] can request support online! button_md: Request support button_link: "{{ support_url }}" - - title_md: General Galaxy support + - title_md: microGalaxy support description_md: > - ... + Users of microGalaxy can submit any kind of bug report via the microGalaxy webserver button_link: "{{ galaxy_base_url }}" button_tip: button_icon: - title_md: microGalaxy chat room description_md: > Of course! Check out the microGalaxy Matrix channel - [microGalaxy Matrix](https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im) - button_link: + button_link: "{{ microgalaxy_matrix }}" button_tip: button_icon: - title_md: Can I upload sensitive data? diff --git a/communities/microgalaxy/lab/sections/7_community.yml b/communities/microgalaxy/lab/sections/7_community.yml index fcef5a9f..1324886d 100644 --- a/communities/microgalaxy/lab/sections/7_community.yml +++ b/communities/microgalaxy/lab/sections/7_community.yml @@ -7,7 +7,6 @@ tabs: - title_md: Chat with other users description_md: > Of course! Check out the microGalaxy Matrix channel - [microGalaxy Matrix](https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im) - title_md: Join our community! description_md: > @@ -19,7 +18,7 @@ tabs: Check out our site and join our community via [microGalaxy mailing list](https://lists.galaxyproject.org/lists/microgalaxy@lists.galaxyproject.org)! - button_link: "" + button_link: "{{ microgalaxy_matrix }}" button_md: button_tip: Visit microGalaxy @@ -35,25 +34,49 @@ tabs: content: - title_md: General support description_md: > - [General Galaxy support](https://galaxyproject.org/support/) + General Galaxy support + button_link: "{{ support_url }}" + button_tip: + button_icon: - title_md: General help forum description_md: > - [General Galaxy help forum](https://help.galaxyproject.org) + General Galaxy help forum + button_link: "{{ galaxy_help_url }}" + button_tip: + button_icon: - title_md: Galaxy Training Network Slack workspace description_md: > - [GTN Slack channel](https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg) + GTN Slack channel + button_link: "{{ gtn_slack_url }}" + button_tip: + button_icon: - title_md: Galaxy Training Network Community chat description_md: > - [GTN Matrix channel](https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im) + GTN Matrix channel + button_link: "{{ gtn_matrix_channel }}" + button_tip: + button_icon: - title_md: microGalaxy user community chat room (Same channel but using Matrix/Element) description_md: > - [microGalaxy Matrix channel](https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im) + microGalaxy Matrix channel + button_link: "{{ microgalaxy_matrix }}" + button_tip: + button_icon: - title_md: American Galaxy Sever chat description_md: > - [Usegalaxy.org chat](https://matrix.to/#/#galaxyproject_Lobby:gitter.im) + Usegalaxy.org Matrix chat + button_link: "{{ american_server }}" + button_tip: + button_icon: - title_md: Australian Galaxy Server chat description_md: > - [Usegalaxy.org.au chat](https://site.usegalaxy.org.au/request) + Usegalaxy.org.au chat + button_link: "{{ australian_server }}" + button_tip: + button_icon: - title_md: European Galaxy server chat description_md: > - [Usegalaxy.eu chat](https://matrix.to/#/#usegalaxy-eu_Lobby:gitter.im) \ No newline at end of file + Usegalaxy.eu Matrix chat + button_link: "{{ european_server }}" + button_tip: + button_icon: \ No newline at end of file diff --git a/communities/microgalaxy/lab/templates/conclusion.html b/communities/microgalaxy/lab/templates/conclusion.html index 9222c682..4e7cb130 100644 --- a/communities/microgalaxy/lab/templates/conclusion.html +++ b/communities/microgalaxy/lab/templates/conclusion.html @@ -1,6 +1,6 @@ {% load markdown %} -

+ {% if help_links %}

microGalaxy community support

    @@ -11,7 +11,7 @@

    microGalaxy community support

    {% endfor %}
{% endif %} -
+ -->

News and Events

From f10b9011930cb76cdaf9476eded5d220484095d5 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Thu, 12 Dec 2024 20:03:55 +0100 Subject: [PATCH 34/38] commenting the news and events section for now and commenting the bottom helping links since we have them aready in the community section --- communities/microgalaxy/lab/templates/conclusion.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/communities/microgalaxy/lab/templates/conclusion.html b/communities/microgalaxy/lab/templates/conclusion.html index 4e7cb130..fdfbc08a 100644 --- a/communities/microgalaxy/lab/templates/conclusion.html +++ b/communities/microgalaxy/lab/templates/conclusion.html @@ -1,6 +1,6 @@ {% load markdown %} - + +

News and Events

@@ -24,7 +24,7 @@

News and Events

-
+ --> {% if feedback_email %}
From bb65e594953d21015a843cb478d40e53b600a2e6 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Thu, 12 Dec 2024 20:59:46 +0100 Subject: [PATCH 35/38] correcting the bottons shaps --- .../microgalaxy/lab/sections/7_community.yml | 24 +++++++------------ 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/communities/microgalaxy/lab/sections/7_community.yml b/communities/microgalaxy/lab/sections/7_community.yml index 1324886d..d4927507 100644 --- a/communities/microgalaxy/lab/sections/7_community.yml +++ b/communities/microgalaxy/lab/sections/7_community.yml @@ -36,47 +36,39 @@ tabs: description_md: > General Galaxy support button_link: "{{ support_url }}" - button_tip: - button_icon: + button_md: microGalaxy support - title_md: General help forum description_md: > General Galaxy help forum button_link: "{{ galaxy_help_url }}" - button_tip: - button_icon: + button_md: Help forum - title_md: Galaxy Training Network Slack workspace description_md: > GTN Slack channel button_link: "{{ gtn_slack_url }}" - button_tip: - button_icon: + button_md: Slack channel - title_md: Galaxy Training Network Community chat description_md: > GTN Matrix channel button_link: "{{ gtn_matrix_channel }}" - button_tip: - button_icon: + button_md: Matrix channel - title_md: microGalaxy user community chat room (Same channel but using Matrix/Element) description_md: > microGalaxy Matrix channel button_link: "{{ microgalaxy_matrix }}" - button_tip: - button_icon: + button_md: Matrix channel - title_md: American Galaxy Sever chat description_md: > Usegalaxy.org Matrix chat button_link: "{{ american_server }}" - button_tip: - button_icon: + button_md: Matrix channel - title_md: Australian Galaxy Server chat description_md: > Usegalaxy.org.au chat button_link: "{{ australian_server }}" - button_tip: - button_icon: + button_md: Request form - title_md: European Galaxy server chat description_md: > Usegalaxy.eu Matrix chat button_link: "{{ european_server }}" - button_tip: - button_icon: \ No newline at end of file + button_md: Matrix channel \ No newline at end of file From 1c6fac3b63d0e1779493b90369678c61cfc5094f Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Thu, 12 Dec 2024 21:05:53 +0100 Subject: [PATCH 36/38] updating bottons shapes --- communities/microgalaxy/lab/sections/6_support_and_help.yml | 6 ++---- communities/microgalaxy/lab/sections/7_community.yml | 2 +- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/communities/microgalaxy/lab/sections/6_support_and_help.yml b/communities/microgalaxy/lab/sections/6_support_and_help.yml index 3906270e..cce7e489 100644 --- a/communities/microgalaxy/lab/sections/6_support_and_help.yml +++ b/communities/microgalaxy/lab/sections/6_support_and_help.yml @@ -20,14 +20,12 @@ tabs: description_md: > Users of microGalaxy can submit any kind of bug report via the microGalaxy webserver button_link: "{{ galaxy_base_url }}" - button_tip: - button_icon: + button_md: microGalaxy support - title_md: microGalaxy chat room description_md: > Of course! Check out the microGalaxy Matrix channel button_link: "{{ microgalaxy_matrix }}" - button_tip: - button_icon: + button_md: Matrix channel - title_md: Can I upload sensitive data? description_md: > No, please do not upload personal or sensitive, such as human health or clinical data. Please see our diff --git a/communities/microgalaxy/lab/sections/7_community.yml b/communities/microgalaxy/lab/sections/7_community.yml index d4927507..ed3cc8ca 100644 --- a/communities/microgalaxy/lab/sections/7_community.yml +++ b/communities/microgalaxy/lab/sections/7_community.yml @@ -36,7 +36,7 @@ tabs: description_md: > General Galaxy support button_link: "{{ support_url }}" - button_md: microGalaxy support + button_md: Request support - title_md: General help forum description_md: > General Galaxy help forum From 61e9a8cad054f7d366fd822e4cb4e7d050400be6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Wed, 18 Dec 2024 12:52:25 +0100 Subject: [PATCH 37/38] Delete communities/microgalaxy/resources/.~lock.curated_tools.tsv# --- communities/microgalaxy/resources/.~lock.curated_tools.tsv# | 1 - 1 file changed, 1 deletion(-) delete mode 100644 communities/microgalaxy/resources/.~lock.curated_tools.tsv# diff --git a/communities/microgalaxy/resources/.~lock.curated_tools.tsv# b/communities/microgalaxy/resources/.~lock.curated_tools.tsv# deleted file mode 100644 index b540fde2..00000000 --- a/communities/microgalaxy/resources/.~lock.curated_tools.tsv# +++ /dev/null @@ -1 +0,0 @@ -,paul,paul-LIFEBOOK-U7410,07.11.2024 12:25,file:///home/paul/.config/libreoffice/4; \ No newline at end of file From 9aac9abe4f5f6c1d70e2367610a91388bae7636e Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 18 Dec 2024 13:11:39 +0100 Subject: [PATCH 38/38] Update communities/microgalaxy/lab/base.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bérénice Batut --- communities/microgalaxy/lab/base.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml index 03d55058..c6a15c65 100644 --- a/communities/microgalaxy/lab/base.yml +++ b/communities/microgalaxy/lab/base.yml @@ -1,5 +1,5 @@ # Request this as a webpage with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/tree/main/communities/microgalaxy/base.yml +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/galaxyproject/galaxy_codex/tree/main/communities/microgalaxy/base.yml # ----------------------------------------------------------------------------- # Use these variables in HTML templates like: